If you have just the pipe coming out of the floor and you need to install the flange, I would suggest the following: First use a sold PVC flange. Cut the pipe so that when you push the flange down, you get good contact with the floor. Since your concern is hitting pex (which I doubt because installers usually leave you some room) attach a few 1/4-20 screws through the countersunk holes in the flange and secure them with nuts so that you have a few "studs" sticking out of the back of the flange. Glue up the flange and push it onto the pipe making sure you orient the slots so that the closet bolts will end up in the right place for attaching the toilet. Once you have that in place, mix up a batch of hydraulic cement in a Dixie cup and pour it into the slots where you will install the closet bolts, filling the void between the flange and the surrounding concrete and encapsulating the 1/4-20 studs. When the hydraulic cement sets, you will have the flange sufficiently anchored to the floor. Note: If you are planning a floor finish other than epoxy, paint, sheet goods or VCT, you will want to actually install the flange on top of the finished floor.
Once you are all set with the flange, dry set the bowl, no wax ring, just put it down in the correct position and see if the rim of the bowl is sitting level, left to right and front to back. If it is not, slide wood shims under the edge of the bowl until the bowl is level and does not rock. At that point tape the part of the shims that you can still see to the floor. Pull up the bowl and install your wax seal and bolt it down.
Mix up a batch of sanded ceramic tile grout, you pick the color, but I wouldn't use white..maybe get something that goes well with your floor finish. Pack the joint between the bowl and the floor with grout and tool it off cleanly. Let is set for a day, then pull the shims out and fill the remaining openings the same way.
The whole trick to a permanent leak proof toilet install is to eliminate all relative motion between the bowl, floor, and flange. The wax ring is a non resilient seal and if the bowl rocks or the pipe floats around, you will eventually get seepage from the seal.
The anchoring of the flange and the grouting of the bowl ensure that nothing is going to float around or rock. One added advantage of grouting the bowl is that in the event you have someone using the toilet that has poor "aim", you wont have piss collecting under the bowl where it will just stink when it gets hot out.
