I had this same experience. Used shims to adjust the spacing on a 6 bolt wheelset to work as backup wheels the center lock wheels on my CX bike. Was prepared to jump through some hoops but only had to ship one wheel and it was a fairly painless process.
YMMV and I don’t know how that would work with neutral support wheels but I haven’t had any issues getting 2 sets of disc wheels to work well with 1 bike.
Am I one of the lucky few with no alignment issues? I have multiple disc wheelsets for my mountain and cross bike, interchange them all the time for racing vs. training, never have to re-align the caliper and haven’t shimmed a single rotor. No rubbing. I know the tolerances are tight, but the spacing specifications for a given hub width are all the same.
You can replace your thru axle with one that has a handle.
Yes and no: if you are really picky you may want to use some shims to consistently have your rotors centered. Rides of Japan and @gpl have made a nice videos about this on their Youtube channels.