I am not quite sure if there was a difference. The "Windows 95" version would still run the game in DOS mode as far as I remember. If at all, then they added a Window 95 compatible installer, but I would not even bet on that
We actually have a superior version now since it can be installed on Windows 7,8,10 and 11.
ps: 16 Bit Windows software doesn't run on our 64 Bit computers.
From what I remember the Win 95 version was supposed to have 'enhanced' audio.
Do you have any reference for that?
I watched a video of the Windows 95 verison. I would have to lie if I said I heared any difference https://www.youtube.com/watch?v=2-4R6eeQSNc
You got me curious however, so I got my hand on the ISO files of the windows 95 version nd compared it with the DOS version (using winmerge, which compares the content of all files).
The source files are identical, also the executable launcher for the DOS version. The windows 95 version has a updated readme, a DirectX directory, a setup utility and a file called RA2START.EXE. That is a 16 bit windows program and therefore does not run on modern machines. Also some system files are different.
Theoretically it would be possible that the game used the DirectX soundcard settings to run with 44100KHz, the DOS version is set to 22050 KHz (you can see that if you 'exit to launcher' then start the 'setup' and 'advanced settings'). But since the source files are in low quality in both cases, I doubt that it makes any difference.
But it's all just hypothetical anyway, that software does not run on any 64 Bit computer and I don't have a 16 or 32 bit computer to test it with and my SB16 is long gone (I have no intention to experiment with a XP VM).
The one thing I could do was to test the DOS version from the Windows 95 CDs, since some system files are different to what we got from GOG. Also this version only supports 22KHz, 640x480 and 20fps.