Removed old leaker toilet, all tile backer and subfloor. Replaced sub, backer and tile and got fairly close to the flanged, black pvc coming up through. It's slightly higher than the tile, but too big to get a closet flange over it to attach to the subfloor by drilling through tile and backer. Don't really understand how to get around this, and I don't want to cut off the pvc pipe that goes down i9nto the floor.

Your black PVC is actually ABS, not PVC but it functions very much the same way but mayb require different glues. I don't see that you have anything wrong with what you describ. The flange can sit on the tile surface or flush with it. The only thing you did that caused a bit more work was tiling under the flange lip requires you to drill the tile for the johnny bolts.

Since I didn't get as close to the ABS all the way around, should I try to put some scraps in to drill through all around or can I use the handibacker or plywood to make sure the closet flange sits level on the tile. The closet flange is touching the ABS, but I think it will be stable when I screw it to the sub floor.

Yes, if you are under the flange in some spots you should shim all around with scrapes of tile or hardibacker and thinset. The flange just makes the air tight seal and is not expected to carry the weight of the toilet and user, that's done by the connection to the floor. Try to arrange your scrapes so you can get your mounting screw between scrapes , cuts down on drilling.