There are different caps for thru-axles.

If you use a non-trainer-specific skewer, make sure it's really secure in the trainer. You do not want to find out mid-interval that the trainer doesn't grip it well and fall over. Also, if your current skewer is "nice", you may want to have a dedicated one to take the scratches. It's honestly easier to just use the trainer skewer; it shouldn't even take ten seconds to swap.