As I recall it, there was actually a minimal set of files needed to trigger the CD to install and you didn't actually need a full 95 install. I worked at a shop at the time and remember doing a lot of reinstalls from those upgrade disks and we definitely didn't spend the time to reinstall both OSs.
I tried searching and the closest I could find was that win95 upgrade would do a full install if you told it to find the old win3.1 on the win3.1 install floppy. I vaguely remember doing something similar, so either it was those versions (unlikely, but possible) or later versions had the same trick.
We definitely did a lot of full windows installs from the upgrade disks without installing the full previous OS first.
