I use bare bottom setups with all my aquatic amphibians, I also find it much easier to keep clean and you don't have the problems of ingesting sand or gravel.
I've used just about everything (except sand), and like the others have said, it's easier to clean. It doesn't affect the axolotl one way or another, as far as locomotion or comfort in the tank (unless they ingest gravel, but we all know gravel is bad).
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