(Thank you to EliGamerX for dumping and documenting the differences!)
What's Different from the Original 1996 Release and Previous Reprints?

In the Disc's Files
*All folders from previous releases have been removed, including all the bonus images and drivers, as well as the PDF manual and Adobe Reader installer in the Ultra 2000 rerelease from 2000. 
**A text verso
*The version of DirectX included on the disc has been changed from DirectX 2.0a to DirectX 9.0b.
*The Autorun launcher present in other Sega Game Honpo physical releases (which are all an emulator+ROM for each release) is used. It promotes and includes now-non-functioning links to the following games that were on the web version of the service:
**Sonic the Hedgehog 2
**Gunstar Heroes
**Bonanza Bros.
**Bio-Hazard Battle (Crying in Japan)
**Shadow Dancer: The Secret of Shinobi
**Phantasy Star II
*The Autorun launcher also does not support installing the game to the hard drive, though the "SEGA-GAMEHOMPO" folder can be copied to another form of storage to run the game from there.

In-Game Changes
*All Compile copyrights have been changed to ones for SEGA CORPORATION; the one on the title screen now takes up two lines as a result. The Quest and Bothtec copyrights are unaltered.
*All credits after the BGM/SE staff for the main game (the main game and Nazo Puyo modes in the PC-98 version of Puyo Puyo and both Windows ports (3.1 and Win32) based on it have separate credits lists, the Classic Mac OS port uses the latter only even in the main game) have been removed, as has the 1993 copyright date (which is also absent from the Nazo Puyo credits).

Other Notes
*Compatibility with modern versions of Windows is improved compared to past releases of this version.
*The keyboard controls may not work in the menu until entering a game.