I just had to fix a couple of flanges due to H.O. wanting to add Tile behind the toilet halfway up the wall "Wainscoating".
Looked in the Kohler R.I. book for the toilets which said @ 12" from finished wall, we would have a 3/4" gap behind the toilet.
So, basic math in my head 12" - 3/8 tile - 1/8 thinset = 11-1/2" > 11-1/4" which should give me 1/4" to spare which isn't much, but for a 1 piece toilet it should be a no brainer.
We set the actual toilet against the sheetrock, measured 12" to center of bolt holes, tried to slide one of the tiles behind it and it wouldn't even fit.
Rough in specs are not always what they're cracked up to be.
If you can fix the flanges, do it, otherwise you may end up with a toilet you can't use.