“I love The Muppets and TMS, however I’m actually not super familiar with all the changes done to later broadcasts and DVDs.”
The big problem is that there is no single definitive version to start with. From the very beginning, there were two different cuts for every episode. The primary difference is the inclusion of the “UK spot”, but there are other little changes for transitions, generally small adjustments for timing. At least one entire song was reshot. Usually, the shorter US cut has short extensions (from a few frames to a second or two), where the longer UK cut will have extra shots. (Note that the masters for both are still PAL; NTSC conversions were always done to the PAL footage, nothing was shot in NTSC for the show.) At some point, a primary cut was created, and they made the strange choice of combining the two cuts rather than staying pure to either one. They took the US edits and cut the UK spots back into them, creating what would technically be a third official edit, and the one which has become the most commonly circulating.
The end credits are theoretically worth a whole separate discussion; the "UK edit"s have credits which are right-justified where the "US edit"s have credits which are centered. The centered ones block a lot more picture, but (as noted above) have become the standard. Foreign language versions generally have a single end credits which is used for all episodes, even episodes which had “unique” end credits. And the final note played by Zoot (the “Zoot tag”) has been replaced numerous times over the years; there are two original versions (the first two seasons and the other three), both of which have US and UK variants. And then there are five or six episodes which have episode-specific unique “Zoot tags”, none of which have broadcast since sometime around 1981, most of which are not currently circulating. [There are about a half dozen more with unique audio, but the unique audio was retained, only the video was replaced, because of repeatedly replacing the superimposed company credit.)
As far as the DVDs goes, Season 1 has issues no matter where you buy it, but the German release is 98% complete and has the longer “UK edits” (mostly with German language credits). Unfortunately, it also has much worse picture quality than any of the other releases. But it has songs from five or six episodes which were cut from other releases. Season 2 is intact (although the Elton John episode has an extra song), and Season 3 is intact except for a few missing unique Zoot tags.