I used to drive myself crazy worrying about setting toilets.
It seemed like an ongoing problem with every new place and leaking toilets.
Over time, I realized most of my past problems were improperly set flanges. Wrong height and crooked were the most common flaws. Previous owners usually tried all kinds of hack fixes and the flanges usually got destroyed over time. Think of your toilet install as a gravity system. It will work properly without clamping the begeezus out of the flange bolts. The "seal" is there for blocking gases. A properly installed standard toilet should flush fine without the seal and not leak.
@Codyboy , You are lucky. You're able to start fresh with a good 4" PVC pipe. In that scenario I like to use a solvent welded 3" inside fit with a slight topside taper for wax seals with plastic liner rings. Your flange height will be great right on top of the tile. Clock the flange whichever way you prefer. Do a dry fit and set the toilet bowl without a seal. I like to use painter tape and mark the exact bowl placement It makes setting the toilet easier without twisting or moving as you compress the seal. Do this before you glue and screw the flange permanent. Some toilets are deformed. It's a crappy deal, but it's reality.
Anyhow, if the toilet sits flat, you've overcome the biggest obstacle.
Slight shimming is ok too, if it's not rocking on the flange.
Use a good bit on your hammer drill when you go through the tile. I like to use a shop vac while doing that part. The bit produces less heat if the debris is removed while drilling.
Let the PVC cement set fully before you do the final install. Set the toilet on your seal and squish it down using weight. Don't clamp with the flange bolts. I sit right on the bowl and rock a bit while squishing the seal. I finger tighten the flange bolts as the toilet settles down. At the very end of squishing, you may still have a slight wobble. I use thin shims to eliminate all wobble. (No wax seal in the world will hold up to a wobbly toilet over time.) After you have the toilet flat and steady, apply a thin bead of sealant around the toilet base. The sealant is there to keep the toilet from sliding around and make cleaning easier. Let that sealant cure before using the toilet.
After all that is done, put the plunger in a locked cabinet or throw it away. Plungers and wax seals are a bad combination. If someone is trying to push a plug past your toilet flange, the seal won't win. Again, it's a gravity system. Those seals are meant to stop gases. Applying pressure with a plunger isn't a good combination. If you don't blow out the wax seal, that toilet will be leak free for years and years. The internal valves and gaskets will go before the wax seal fails.
BTW, if anyone has a toilet that is moving or sliding. The seal is probably leaking already. Pull the toilet and set it properly. It will save you floor replacement if you catch it in time.