I think server problems we had on release might have played a factor.
I obviously need to have all versions installed for testing, and they work just fine so, more than a conflict per-se, it's more like the Live Update (because of server slow sync issues), not being able to completely overwrite files which were previously P3D-only, with new ones that are supposed to be cross-platform, so you were stuck with one or more P3D-only files which failed to be updated, which would cause all sort of issues in MSFS.
Instead, starting from scratch, you can't possibly run in the issue of P3D files still there and not being overwritten as they should, so it will always work. But I'm fairly sure this will be fixed shortly, both because servers are finally catching up, but also because we'll release a new P3D full installer that shouldn't be reliant on a subsequent online update to fix everything, because it would already *contain* all cross-platform files.