I'd still like to try to address some of the issues, just haven't found the time yet. Widescreen code was ported from ThirteenAG's widescreen fix and baked directly into executable files, but it's a bit buggier than I knew initially. I fixed the bug with 1600x900 resolution and there was also a small bit taken from the the very first widescreen fix that ever existed for the game. I have to remember to credit the person in the next version's changelog, without that bit, it craps out at higher resolutions, such as 3840x2160. I haven't noticed 1280x1024 resolution's broken as well...and there's the thing with broken weapon inventory icons in the first game.
Regarding version 1.04, from what I remember, it had some cosmetic fixes only visible when you read its code. Don't see how it could cause freezes compared to previous version. Maybe it's something inherent from the original game combined with some undetermined system specific.
Regarding patch stopping showing configuration dialog at startup; that's actually a good thing as it was intended to show by itself only when settings couldn't be read from the system, which most of the time can happen due to permission issues since the original game stores them in the part of Windows registry where only admins have write access. Windows has some compatibility workaround for such cases, but they could fail under certain circumstances.
Autosave checkpoints; I've no idea how they fail to work for some people. I don't think it has anything to do with Windows version, they work on my end on anything from Windows XP to Windows 10.
Small notes at high resolution; it's strange that they don't scale like other elements do. No idea how to fix.
dsound.dll included with GOG version is older version of IndirectSound, which happens to have some issues. It's not needed to fix issues with missing and dropping sounds as those are addressed in the patch. The only reason to use it (latest version, of course) would be if you like the way it mixes sounds better compared to Microsoft's implementation. I think an actual surround system is needed to hear the difference.
Finally, regarding GOG Galaxy, I've never used it and can't tell why launching patched game through it wouldn't work. Can anyone test if renaming dinput.dll in game folder to something else makes it launch? It'll partially cripple the patch; redirection of user file read/writes operations to user specific folders and settings in Torque.ini won't work. If it helps, then it should be fixable.