The plumbing vents probably don't have boots on them, and the wall to roof flashing probably isn't done yet, either. Many of the trims and flashings are done in a certain order, so if the lower roof isn't done yet, it isn't flashed yet. The final wall flashing goes over the lower roofing metal. Likewise, the ridge isn't weatherproof until the ridge cap is on, although usually they cover it in underlayment, then remove the underlayment from the inside once the ridge is in place if it is a vent-type ridge. It's really too early to tell if they've done something wrong.

I am not a roofer but have hired many roofs repaired and replaced. This I can tell you. After replacing a skylight on a torch down roof there shouldn't be a screw head on top of membrane. Any visiable screw should be in the shadow of skylight flashing and at least 3" above horizonal surface of roof. "IF"you are able to stop a skylight leak with caulk,it will soon return due to expansion and contraction of all the different material involved. The more i hear,the more it sounds like you need a different roofer. As if you don't have enough trouble,I have somthing that will distress you even more. Leaks so small they seldom or never drip indoors can and will rot the structure out. Out of sight,out of mind roof leaks are to building what cancer is to humans. Use good roofers,they are cheaper over the long haul.

and Zahner Zinc could possibly stamp out some custom metal roofing if your roof pitch is steep enough. Or a decent sheet metal shop can bend up sheets of aluminum and do flat lock similar to millenium but in larger pieces. It's hard to get good installation with metal. They like to use a lot of caulk joints, which defeats the purpose The aluminum standing seam they keep telling you're thinking of is "Galvalume" style which is steel electro plated with aluminum somehow. Galvalume is still "ferrous" and would rot by the ocean if it found a good galvanitic reaction with something. What you meant in your title was "non-ferrous" . If you have a roof made from stainless or a non-ferrous metals like zinc, copper, aluminum, and it looks correct to someone who knows, there is no guessing as to how long it will last undisturbed.

A proper roof is also very important, because leaks, cause rot, and numerous other problems, that can cost you a whole lot more money to fix all the damage than you would have, if you just had that fence pulled down and repaired it now. Since the diy previous owner, obviously was creative, but,had no real diy talent to go with it, it is probably a very good idea to get the foundation of the porch etc, inspected too. I would have that done before doing the roof, because, there is a possibility that it is unsafe and needs to come down or have supports added. Oh, and by the way, dont worry about the weight of shingles, that porch, is obvously holding a whole lot of weight right now. Have you ever moved a treated fence panel? They are not light weight. There are several of them up there too, which is a whole lot of weight,and when they get wet in the rain, double that amount of weight. It is totally unbelievable what some people do. I am guessing you didnt have a home inspector when you bought it, because, pretty sure that would have had to be corrected. There should have been plywood put on that roof, before the metal, and that would have deadened the sound of the rain. Bare wood, meeting rain, is always a no no. Good Luck to you.