This is our second house with skylights and ours do not stick out that far. In ours, that second layer from the top, is up against the roof. It looks like they built up a shaft, above the roof, to place the skylight into.

Found a photo online -- ours were like this. See no built up framed box below them.
http://www.designerstaircases.com.au/images/services/Skylights/skylights6.jpg

Another photo:
http://raysroof.com/wp-content/uploads/2016/05/skylight-installation-new-york-homes.jpg

Not sure why your contractor raised them up above the roof like that. Show him these photos and ask him why.

We have skylights over our covered porch and they don't look like that at all. I'll snap a photo later & post. I'm sorry yours turned out like that, but I am sure there is a fix!

The curbs on those almost look like they are the type made for a flat roof (taller curb by design), not a normal pitched roof. What model, and flashing kit was used?

There are two types of skylights--deck-mounted as linked in chispa's post--and curb-mounted, as in the subject of this thread.

Visually, it's a bad choice to use curb-mounted skylights where they're so visible. And it doesn't take an expert to notice that the installers bent out the flashings on at least two of them.

The curbs on the brand I've used in the past are much less obtrusive than the ones the OP has used and include a smooth finished surround to cover the flashings along the sides.

IMO wrong product used for this install

Check with the manufacturer. Often the curbs can be made from 2x4's or 2x6's. Most builders/roofers make them from 2x6's because the flashing doesn't need to be trimmed on site. If it's of no consequence to the finished product, then 2x6's are more convenient. Yours look to be made from 2x6's and if you check with the manufacturer, you might be able to reduce the height 2" by redoing them with 2x4's. It's not an easy job to change them out to 2x4's after everything is in place, but if it's important to you, then it is quite doable.

Those skylights are very blocky, angular, and high profile as well. Another product, like a Velux skylight, has a much lower profile and sits lower on the curb (worthy's photo in a post above) and that might be another option for you to consider. (If you change over to Velux, you'll also have to change flashing to retain the manufacturer's installation warranty, but with a 2x4 curb and the lower profile skylight, I'm guessing you'll be able to reduce the height above the roof by approximately 3".) If you're intending to replace the make of the skylight or the type of skylight with deck mount, make sure the inside curb/rough opening dimensions are the same or you might be adding significantly to the cost in unexpected ways with framing changes.

In terms of positioning: I might be mis-interpreting the photo, but unless there are other considerations with obstructions, etc., usually the best location for skylights is in a position favoring the center or dark part of the room to complement the light from the windows. It's what skylights do best: bringing light into the center of the room. Hindsight is 20:20 right? Having three positioned near your windows won't do a lot for you in comparison to the two that you say are already positioned back further in the room. Without seeing the overall design, I suspect my choice likely would have favored just two larger skylights back towards the center/rear of the room negating the need for three 2x2 skylights at the windows. If you do refit the skylights, it might be worth considering repositioning some or all of them back up the roof a ways to bring light into the center of the room.

Yes, and the installers didn't take their time with the flashing. Just got sloppy. If they are re-doing the curbs, they may have to re-order some flashing and make sure they take their time with the next install to get the flashing seated tight and trim as necessary so that it doesn't protrude above the curbs and get flexed by the skylight and/or the mounting screws when it is in position. If you choose to retain these skylights, then fixing the flashing issue shouldn't take them long at all and you should expect it.

Personally, all else being equal, I prefer to recommend curb mount skylights. They take longer and are more involved to install and drywall on the inside. But the trade-off is that at some stage, homeowners are going to need a new roof. In my experience, the majority of roofers are far more comfortable reinstalling a roof around an existing curb mount skylight as opposed to a deck mount skylight. There's less room for them to screw up and they usually have the materials on hand to make flashing repairs/replacements. Deck mount skylights require that someone on the roofing team reads and becomes familiar with the installation instructions and the chances of that occurring are somewhere between slim and none, and the materials necessary for repair are not necessarily in the roofers' on-site toolkit. Roofing crews that know what they are doing around skylights are worth their weight in gold.

At this point you have a couple of choices: 1) Live with the curb-mounted skylights and the clumsy installation, or; 2) replace them with deck mounted alternatives.

It may be possible to remove the skylights and reduce the curb heights somewhat.

Good luck!

@worthy can you possibly send me a link to the Velux smooth finish surrounds? I've talked to two people at Velux and neither know about these. Is it a Velux product or third-party?

Yes, as many of the commenters noted, they are 2x6 frames, so he offered to take them down to 2x4. The other issue, as I tease apart this problem, is that on these three skylights, the flashing is Velux, the skylights are a different color and brand (still trying to find out what) and the screws they used appear to be a third texture and color.

On the two skylights further up on the roof (that project into the family room itself), they used Velux throughout and now that they've been taken down to 2x4's, it's a much cleaner look.

Someone at Velux suggested taking the off-brand skylights to a car finisher (since they have to come of anyway to reduce the height of the curb) and having them match the Velux color. Then we can also use Velux screws to mount back on. This seems like the easiest solution towards a cleaner look without having to rip off part of the roof, which my contractor is refusing to do. Would love to hear your thoughts.

can you possibly send me a link to the Velux smooth finish surrounds?

The screen grab--about 16 minutes in--is from this detailed installation video done by Velux and currently available on their Canadian site. There's no suggestion of any third-party suppliers.

Since the three skylights pictured aren't Velux, it's unlikely their surrounds would fit--even if you could buy them separately.

Aluminum eavestrough and fascia installers could probably fashion smooth surrounds on-site. Best bet is if you see one of them working on a nearby property. Or you could try a local roofing supplier with sheet metal bending equipment (brakes).

Once you cut the curbs down though, it may be improvement enough.

Velux flashing is wonderful. It's a shame you have a different brand of skylight on there, because as a package, for its skylights and flashing Velux provides a 10 year no-leak warranty. Contractors love it. If the skylights leak within 10 years of installation, assuming the skylights were installed according to instructions, then it's on Velux and not the contractors. If anything leaks on skylights, it's typically out of sight under the shingles at the junction of the skylight base to the roof decking, so having Velux flashing is great. I'm thinking that after cutting the curb to 2x4's and a re-installation, your contractor would appreciate this too.

Velux mounting screws are black coated aluminum, which is a different color from their skylight frames and flashing, but it blends in. I wouldn't try replacing the silver screws on those skylights (if that's what you have in mind) otherwise you're likely to invalidate the warranty and cause a break in the glass seal. You might consider just dabbing on a little paint. Take a can of spray paint that closely matches the frame color onto the roof and spray a little onto a small, cheap brush and dab it on the screw heads. Be careful of overspray on the glass.

2-part auto paint on the skylight frames will be expensive. Might be cheaper to get new skylights.

Nice to read that you're getting your issues resolved.