I had the very same problem with my first child, and now again with my second. Here is what I found that helped:
-based on No Cry Nap Solution book, go in just before 35/40min wake up time and use a method that helps 'coach' them through the wake up. I tried shushing, patting bum or back, re-soothering, or slightly bouncing mattress beside them. Each were different and just tried them all til I found what worked. It usually took 10-15min to get them through, and wouldn't always work but after a week or so it helped.
-once baby could roll onto belly, both definitely preferred to sleep this way. Found it was easier for them to START on belly rather than start on back (as I was always doing) because at the 35/40min mark they would each attempt to roll to belly but would wake up too much.
-sadly it was mostly time and a lot of coaching effort to get them into it, but totally worth it.
Keep trying and Good luck!