If you size the chain for 50:28t and adjust the derailuer B-screw for that cassette you'll probably get good shifting on the other cassette with no issues. I swap between two wheelsets, and it doesn't require any adjusting. The do sell cassette shims for fine tuning, if it doesn't work right out of the box.

The main issue is the rim external width needs to match fairly closely (<1mm) or you're going to need to adjust the brakes every swap. My rims have ~2mm differences, and the brakes are useless on the narrow rims. Its a trainer, so I just ignore it, but certainly wouldn't work for real riding.