Yes, the worms can be beaten. Focus on avoiding their attacks by paying attention to the pebbles they spurt before their attacks, and getting in hits where you can do it safely, rather than tanking through hits - Crisis Point's combat is focused around mobility and dodging. As you already noted, destroy the rocks to get health when you need it, and make sure you purchased the Skill that pulls in health pickups and doubles the health gained from them, too.
As far as Steam goes, sorry, but no, I will not be using it as the default customization. Their controller tool has caused me far too many headaches already to put any trust in it as a developer, with how often I have to troubleshoot somebody's gamepad not working, only to find out it's because Steam is messing everything up. That doesn't mean you won't be able to use the tool of course, you still can, but I will be keeping all of my current controller customization options, as well as any future options I implement, and using those for the Steam release.
I can understand why the button prompts being different may be confusing, I use a DS4 myself and it took quite some time to be comfortable with the Xbox prompts that most games use, but Crisis Point very rarely uses button prompts - they're only really there for the initial tutorials - so until I find the time to implement an in-game method for configuring which button shows as which prompt, it wouldn't be too difficult to just ignore the prompts for now, since you're almost at the point where tutorial prompts pretty much stop appearing.