If the flange is secure, you actually can leave the flange "as is" with the layers right under the flange ring. I write that because if you damage the flange it can create a whole new can of worms if the flange or flange-to-pipe connection was damaged and had to be repaired/replaced. However, I'd cut the plywood back closer to the flange, I'd cut back at least to the same size as the first layer that's on top of the plywood in the photo. You might find that the closer to the flange you cut, you can then dig out the layers under the flange. If you get there, then you can simply install new layers of your flooring sandwich around the flange. The new layers don't have to go under the flange, the new layers can encircle the flange. However, if yo have, say, a 3/4" gap between the top of the subfloor and the bottom of the flange, then just cut some small wood blocks (say four blocks, 1" square and 3/4" high for example or sized as needed) that will fit snugly between the flange and the subfloor, and set the blocks around the flange at the 3, 6, 9, and 12 o'clock positions. Keep the blocks clear of the flange bolt locations. The flange itself should be securely attached to the waste pipe beneath. Use a putty knife or equivalent to scrape away the residual wax. Toilets are pretty easy to install, but if this is your first time I do have a recommendation. Use a waxless adapter. Something like the Fernco. Size the waxless adapter to the size of your waste pipe. The thing is that wax rings are "one and done" things. If you set the wax ring, then set the toilet, but then you have to pull the toilet up again to reset it, technically you would want to scrap away the deformed ring and install a new ring, even though the ring you just installed is only 10 seconds old. Once a wax ring is deformed you can't really count on it to give you a good seal the second time the toilet is set. With the Fernco, you set it on the base of the toilet. Then you can set the toilet, pull it, reset, pull, reset, etc. It's good forever, so to speak. You can set a toilet that is fully assembled. Again if you think the weight might be a problem, you can remove the tank from the bowl. then just position and set the bowl. Then reinstall the tank on the bowl. Then shim the base, snug the bolts, and there you go. And as always, do NOT overtighten any of the bolts that go through the china. Snug them up but don't crank down so hard that you overtighten them. You don't want to crack the china. If the base wobbles on your new floor, don't try to make it wobble-free by cinching down hard on the flange bolts. Use toilet shims between the tile and the toilet base. Then snug up the flange bolts. Buy a new set of flange bolts too. Good luck and happy toileting!

Well you can do it either way. If you know the height of your tile you can install the flange up to that height, or you can wait until the tile is laid. They have pieces to make it higher if it's two low. I prefer to install it first.

Well, it's a 100 yr old house. The cast iron wc is not supported at the flange, though it's very rigid. Perhaps there's a horizontal arm that is braced between the joists, and the whole thing is resting on that, but I can't tell. Anyhow, it's rock solid. As for flange extender... there's no gasket or anything that came with this thing, and I got it at a plumbing supply house (Oatey white extender). I just got back from HD to try to get one. They didn't have gaskets nor gasketed ones of any sort. The "master plumber" who had been at this house also left an extender there which also is just black hard plastic - same thing. So I'm thinking of either applying some wax between the flange and the extender, or maybe even plumber's putty (what do you think of that?) Perhaps some silicone is another option. One more thing: HDepot had a fluidmaster product for low flanges that was a "wax-less" gasketed assembly that fit's into the drain, which also has a thin rubber gasket at the top. The toilet just sits on this thing, and they claim that it's for low flanges and uneven or tiled floors. Anybody tried this thing? BTW, the ones they had on the shelf were apparently returns (retaped shut), and you could tell that most buyers couldn't figure out what to do with the extra O rings that came in the boxes - the directions on the box don't even mention how to use them (it's not at all obvious with this contraption). Thoughts on this "waxless" thing? I'm afraid to try.

catbuilder, What did I say? I said I don't want to drive him off the edge; he's already close to going out of his mind from the kitchen remodel that is also happening right now. But I also say I won't go for a hackjob. Decision time is 1-2 weeks away it looks like. oneandonlybobjones, We have a plumber we already use for stuff like this, and I'm thinking he'd probably quote $300 for this job, which DH thinks is money not worth spending (and of course, I disagree). My wifely instincts are telling me that if I wait a few weeks DH may be willing to revisit the issue, otherwise he and I are gonna be at a stuck point because unless there is a proper solution that doesn't look like a hackjob I'm not gonna go for it. Closest thing so far is the toilet riser but it's plastic, which is a no-go in my book. I'd go for it if it was same material as toilet and less than $300. I'm really shocked though that it appears that there aren't already toilets manufactured with high bases. I have contacted 2 toilet manufacturers so far and got no response! Wow!