Yes you can get two wheels to be identical, or close enough, to be able to swap wheels without adjusting anything. In theory the hub/cassette spacing should be identical so you shouldn't need to adjust the derailleur.
For shifting the critical spacing will be from the inside face of the frame dropout to the smallest cog. This spacing can be adjusted by adding thin shims to the freehub body to move the cassette slightly to the right. Both of your wheels will support this.
The procedure to adjust the shifting:
Adjust the derailleur for the first wheel and then replace with the second wheel. If shifting on the 2nd wheel is slow to the smaller cog, then the fix would be to move the cassette farther left but this is impossible. So your 1st wheel needs a cassette shim. This will move the cassette slightly to the right.
If OTOH the 2nd wheel's shifting to the larger cogs is slow, then the 2nd wheel should get a shim to push the cassette slightly right.
Alternatively you may find the two wheels are almost identical and you only need to make a very slight adjustment to the derailleur cable tension when moving from one wheel to another. I have this issue with two sets of 11 speed wheels and an Ultegra setup. The difference is roughly 1 full turn of my cable adjuster - very minor.
Similarly there are shims available for disk rotors. The spacing between rotor and pad is very small so there is little margin for manufacturing tolerances.