I'm waiting for an answer on this one too. The SL-20 we just bought at work has all kinds of dire warnings on the side of the machine, describing world annihilation if you dare put some fixed length stop in there.
I haven't seen them but, I imagine that there is a class of hard stops that attach to the end of the drawtube. I suppose if the collet were pulled into one of those, it could potentially cause damage. Of course, I also have to wonder why the machine wouldn't just achieve its hydraulic clamping pressure and assume that it had clamped up.
My guess is that the collet stop you're using is harmless. I'm with you; I can't see any way that it could damage anything.
Then again, it's not a fixed-length stop (its Z position changes with the collet). So unless you have one of those super expensive dead length 'push' collet closers, all you're doing is getting a so-so depth stop.
Designed for power chucks, not collets but, I found this the other day. Kind of interesting. It attaches to the swarf cover on a power chuck and gives you a positive depth stop.