the main problem is that stable and nightly share the same configuration files/folder
In pcbnew some settings are not correctly read when switching from stable to nightly and back (i.e. copper color layers get switched/messed)
One option would be to see if the portable version is usable (this would be the best IMO in Windows)
or if you can accept a lack of performance, use one version under a VM as suggested in the post above.
One great option would be if Nightly would use a separate setting folders profile as i.e. Firefox is doing for stable and nightly.
But this should be evaluate by developers