While paper towel ingestion is a potential risk, it's a VERY small chance and something that is totally avoidable if you supervise feedings.
I use paper towels in all of my enclosures. I use the Bounty select-a-size personally, and use it in 2 layers, enough to cover the bottoms and I leave about an inch extra on each side to curl up the very bottom of each side. Set the water bowl in the middle to hold them down.