The flange should be mounted on top of the finished floor. Is the first picture of the finished floor and the flange has been recessed? It might require a thicker wax ring, but my guess is that a standard thickness might still work.

Make sure the flange location matches the rough-in spec for the toilet (most common is 12"). Measure from the center of the flange to the wall in back. Then buy a standard installation kit that includes the wax ring and two bolts with decorative caps.

Most supply pipes are standard 1/2" copper, but that picture looks like clear flexible, unreinforced plastic line. I would not want to trust that for continuous pressure for a toilet. PEX or CPVC would work.

I'm also not sure that supply pipe location will work with a standard toilet base because its too close to the toilet centerline and it would be under the base. Having the supply pipe coming through the floor is not common. Most of the time its mounted about 7" up, and in the wall behind the toilet.

Bruce

Hey Bruce. We were totally thrown off by the placement of the supply line and not being able to tell what the material is. Luckily I think I found a toilet that works around where it was placed and I think it was placed there instead of on the wall because the wall is an exterior wall. We are apparently being told from the plumber that he did use copper so I did just asked if it was chrome plated but can you think of what else that could be? Would it be smart to use a flange extender and then a wax ring?

Now I’m being told it is chrome plated brass.

I don't think it is that strange to have the supply in the floor if the floor is wood. Whatever. I thought it was chromed something. Guessing the grey plug (the whole thing) comes off and something will go on it depending on the thread size, a shutoff valve. The line to the tank should be flexible. There are extension rings, plastic and such, but a thicker wax ring (or one of those sponge foam types) will do.

Based on the pictures, I also think you just need a thick wax ring. Its not unusual in renovation tile situations to have the floor a fraction of an inch higher than the flange, and it still works fine. The toilet installation kit for the thicker wax ring should also come with longer mounting bolts. Also buy a package of plastic toilet leveling shims so you can make sure the base is evenly supported.

You can buy a sharkbite 1/4 turn toilet valve and it should work on any type of 1/2" pipe. I used to have reservations about sharkbite fittings, but have found them to be very reliable. In this case its also exposed and it would be easy to see any leak.

Bruce