I may have the worst case scenario for wheel swaps. This is on an old bike (1982), for which I have one wheelset that's clincher, with a freehub and 6 speed cassette, and another that's tubular with a 6 speed freewheel. Both hubs are Shimano, no more than a year or two apart in manufacture, but the cogs are SIGNIFICANTLY displaced relative to each other. So much so that I need to make sure to adjust the limit screws when swapping, or 1) I can't reach the lowest cog on the tubular wheels, or 2) shifting to the lowest cog on the clincher wheels sends the chain right into the spokes. So I don't swap often!

Thanks for all the advice everyone, tried it today, brakes rubbed so had to clean pistons and push them back in as they had auto adjusted to the width of the older discs, the gears 'work' but certainly need some adjusting. I was hoping the set ups would interchange seamlessly as I'm a bit of a lzzy git but I think the lesser of the evils/ least amount of faff is to use the one set of discs and cassette on both wheelsets. Thanks again for all the great advice.

If the cassettes are the same number of speed and same brand, you shouldn't need to make any adjustments to the shifting if everything is set up right. If you're having shifting issues when swapping, one of the cassettes probably needs a spacer to position it the same as the other. I've found that having the same rotors on both wheelsets tends to minimize brake adjustment issues.

Why? He already has an 11t cog on his other cassette.
FWIW, I have two sets of rear wheels, both disc, both using the same brand of hub and rotor. One is my "Upstate" cassette (10-36 12spd SRAM) and the other is my "LowCountry" cassette (10-30) No issue at all with rotor alignment. I use the same chain and just adjust the B screw with the tool. I have never had to fiddle with chain alignment on the RD.

Has definitely been an issue for us swapping wheels on our tandem. Despite exactly the same hubs and rotors, the discs always rubbed changing between wheelsets. Eventually got them adjusted so they swap without rubbing. With some effort, and possibly shims it’s surmountainable, but it can be a PITA.

I worked at a very high end shop. I dealt with Shimano, Campy, Enve, White and Chris King hubs daily. You can declare whatever you want, but my experience is that the precise location of the rotor mount down to a fraction of a mm is not an industry standard. Usually within a brand they are the same.

But I'm sure you have seen more bikes than I have.

That’s a great pun