Set a toilet flange before laying tile, overcompensated by almost 3/4". I cut some plywood to wedge under it, and my only thought is to run a very thick bead of caulk in the gap and hope I make it look halfway decent. Has anyone ran into this issue before, and is there anything else I can use to fill this gap and make it look good?
One solution is to trace the toilet base on a piece of 3/4 plywood and carefully cut the shape out. Place the plywood with shape removed around the flange mimicking the outline of the toilet.
When you have it placed in exact position secure the cutout to the floor with tape and fill the area with sanded grout. When dry remove plywood form, set toilet on the bed of grout.
Mix a bit more of the grout and dress the edges with this. Neatly sponge the area and you should have a decent looking durable base under the toilet that will last a long time .
Never seal around the toilet to the floor! You then sacrifice the ability to see what could become a major problem. If the wax ring goes out, you will never know and that can lead to major repairs down the line. Never seal or caulk around a toilet base ever!
Just fix the real problem, cut the flange out and replace, too low? Shim kit or tall flange kit, never double wax ring, and never seal the toilet to the floor, you are begging for disaster down the line. Just fix the actual issue, don't disguise it.
So I went ahead with the grout under the toilet. I actually put the wax ring on, cut my plywood about 3/16 smaller than the base, set it, leveled it, then filled with grout. 2 days in and it looks great, gonna finish it with grout seal to brighten it up (almost matches the toilet color already). Thanks for the tips guys. I'd recommend this procedure to anyone else that runs into this issue.