It's the way that older version was installed since no one had optical drives on their systems back in 1990. They were the lastest for audio devices following dvd players at the time 3.1 was first seen.
For old 8bit and 16bit dos games and apps that don't even need a dos partition to run off of one free DOSBox program does well there. How about seeing an old 1990 dos game run on Vista?
All the files are right there on an NTFS primary. The utility creates a virtual dos environment where you mount a virtual drive in order to see the old game there as well as other things run independent of any newer OS.
Windows 3.1 like any other old dos program seeing more then one disk was written to look for the next one. I once attempted to simply burn all files from the floppies onto a cd to see if that would work without an iso file and the installer would lock or might not even start.
The fast way to see 3.1 go on is to take a spare drive without anything on it and create a small 1gb Fat16 primary at the front end with a dos startup disk using fdisk there. That will mean unplugging any other hard drives to force fdisk to see that only.
The free Linux drive tool GParted can also be used to see the partition created and later formatted when booting with a dos floppy using the format.com seen there and the format C: /s command for both the format and transfer of the basic dos files. Once you have that done run the set of floppies to see the progressive floppy swapping installation proceed.
Don't you love those old fat based installers?!