If you install the disk version patch over the download version you would also loose support for widescreen resolutions and resolutions higher than 1024x768.
When Larian updated DD for the Steam release there were problems with some of the backups, so they ended up having to re-do the higher resolution support, rather than just make a couple Win 7 compatibility fixes (Hatching the Anthology
). There wasn't time to do a full bug fix / QA procedure. They have since fixed the music bug in the download version (see here
), but the remaining issues are predominantly minor and/or relatively rare; many have fixes or workarounds if encountered, and some, like the overpowered scorpions, wouldn't be fixed now, anyway (being in so many walkthroughs, etc, as a strategy for tough fights).