I think the Aligner clamp is actually better-suited for use with bench stones, instead of the dedicated rod-guided hones. Don't see any reason why it shouldn't do well with a waterstone, so long as the height of the stone isn't an issue. I don't have any waterstones, but some apparently can be some pretty tall 'bricks'. If so, might need to improvise a platform to elevate the clamp to a suitable working height, relative to the stone's surface.
I have used my Aligner clamp with an 8" DMT Duo-Sharp hone supported on DMT's base for those, and really liked the combination (wish I'd figured that out a long time ago).
David