Flooring – Addressing un-level floor when using ceramic tile

By "no other covering over it" - I assume you mean you didn't properly prep the sub floor, and so you put down ceramic tile over an uneven surface.

Which means you didn't "develop" an air bubble (an air bubble won't form under inflexible ceramic tile like it will under vinyl), but rather, you put the tile down over voids, so there was nothing to support the tile.

The ONLY fix for this is to remove the tile completely, level the floor (I suggest floor leveling compound), then put down a layer of Ditra (orange grid flexible underlayment that protects the tile itself), then the appropriate depth of mastic and re-tile.

There is no other way to fix an improperly prepared subsurface when dealing with rigid tiles like ceramic.

Lots of questions (related to this Meta discussion). I will just tackle a few points I feel confident about answering.

Subfloor

The Schluter DITRA does not need to be on CBU so I would skip the 1/2" layer of cement board you are planning on using and make your plywood subfloor thicker (or just skip the CBU and keep your 23/32" OSB). CBU is not "stiff" enough to be a subfloor, it can be used instead of DITRA but it must be secured to a subfloor. It rarely makes sense to use 1/2" on the floor unless you are trying to make the finished floor come out to some specific height (for example to help the transition to another room with a different floor). If you are not goin gto use DITRA, you will want some CBU on the floor but the 1/4" stuff is fine.

Apply the modified thinset and DITRA directly to the plywood subfloor. Checkout Schluter's DITRA Installation Instructions for details on the subfloor prep and how to secure to DITRA to the plywood.

Toilet

Without a picture or diagram it is not really clear to me exactly what the issue is with the toilet drain, but that won't stop me from taking a guess :)

You may be right about getting away with cutting a larger hole in the subfloor to handle the bend of the toilet drain pipe. Are you sure the PVC drain will stick above the finished floor? Realize that the thinset between both the subfloor/DITRA (not very much) and DITRA/tile (more so) will add a little to your height, maybe between 1/8" to 1/4".

Have you measured the height of the toilet drain with the flange installed (just dry fit it to take a measurement)? The flange can be installed on the top of the finished floor (tile), on top of just the DITRA, or on top of the plywood subfloor. In your case you would probably want it as high as you can, so install the tile first and then glue the flange to the PVC closet bend. I think once you dry-fit the toilet flange you will see you are OK here.