The graphics/sound in the cutscenes were slightly improved over the floppy disk release for the DOS CD release and the later Windows 98 CD release with DirectX rendering switched out chunks of the cutscene graphics with new ones, specifically the stuff with ships, if I recall. I haven't played any of the three versions in a long time and none of them work even slightly well on the latest Windows without a bit of work, so my memories are rusty at best.

No idea about the cut-scenes between floppy and cd, but I think only the CD has the "New Missions" option which replaces some of the original floppy versions with easier versions, as the originals were deemed to be extremely difficult. The Windows 98 version runs on the X-Wing Vs Tie Fighter engine and is basically a full on remake. Though I personally don't care for it as doesn't have the dynamic MUSE music system and just has prerecorded music tracks that loop.

In the meanwhile I noticed that the music / sound is quite a bit different. Visually I didn't see any change to be honest. Also noticed that all the briefings are spoken in the CD-rom version. This was not the case in the floppy version.

The 98 releases do have iMuse, but it uses the audio clips from the JW scores instead of the game score. For the Alliance remake of the games, the MIDI music was revamped with current sampling, recorded and restored as the game music, working as it did before and sounding great.