If he is actually getting stuck, then you should do something, probably remove the lilly. You could possibly replace it with other plants. But if he is only hanging out there, then there should be no problem.
Just be sure to watch for normal behavior, going up to breathe, at least some swimming, reaction to feeding (he should quickly and actively go after the food when added), and (at least for the bettas I've had) they should be "interested" in what you are doing around the bowl. Being interested almost certianly means begging for food. If he acts normal, other than floating in the roots, I'm sure he's fine. Mine usually like to hang out the floating moss I keep (java moss).