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.
There are (at least) two different types of stains for concrete. One is a surface coating, the other is acid etching.
The former can work, but isn't as durable/lasting. I believe most of the products you get at the big-box stores are more of a top-coat type of stain.
Acid etching is just that, it's a stain containing an acid that actually etches the concrete. This is the typical type of stain you see in home magazines and such. The etching provides a deeper stain that is more durable and not prone to flaking.
I've done the latter, and applying it is super-easy. It's the prep work that can be a chore--namely if you have adhesive on the concrete already. In our case, we has tile mastic, which we had to dissolve using soybean based stripper. It worked great but was incredibly messy.
If you don't have glue to deal with, however, you should be good to go. Order up the stain (lots of places online to get it). You then dilute it per instructions and spray it on the concrete. I used a garden sprayer for this. You then let it sit for a period of time, and then you apply a neutralizer to stop the reaction.
After that, you apply water and mop/squeegee/wet-vac it up.
Then, you apply a sealer of some sorts. Common options are wax-based, polyurethane, and epoxy. I went with poly as it was relatively easy to apply (roll it on). That said, I don't think it was ever truly waterproof. For your needs, you may want to go the epoxy route.
Best Answer
Recommendations vary because conditions vary. Here are the primary factors:
The point is that no one can give you a number. You'll have to either rely on look and feel assessment or use sensor hardware to measure moisture content. Also, follow the paint manufacturer's instructions. Some coatings are more tolerant of substrate moisture than others.