The thread's old...and so am I!....but we're still around.
The issues with clean installs are indeed a more serious consequence of this disc enumeration "quirk." (That was largely the focus of one of my later posts.)
Generally speaking, though, you shouldn't need to actually remove
the other discs to force Windows onto a particular drive. Selective disconnection, or disabling SATA ports in the BIOS (when that option's available) are usually adequate. But even given that, I completely agree with you....it should never have been this hard.
If Windows Repair literally does not see your Windows drive, that would be a different matter (as apposed to the confusion of not being able to discern which drive/partition its on from the list, due to changing disc enumeration).