Well, I have both of the TG-100 (which is beat all to hell and back, but still works like new), and TG-300 midi modules and the TG300B mode on my unpatched MU2000 sounded VERY different from them. Once I upgraded the firmware on the MU2000 to EX, it changed the overall sound of the TG300B mode to something that sounded almost like my SC-55 and SC-55 MkII and the old TG300B just didn't sound like them. I also know that some of the known facts in English sights are wrong and I can only assume that because the MU1000 and MU2000 were never released and supported outside of Japan. For instance, I know I have over 1600 instruments on mine since the EX upgrade (and not including PLG cards installed in the unit), but the wiki only states that there are 1396.
I guess somebody is going to have to get a MU2000 without the EX upgrade, go into TG300B mode, and record a bunch of songs. Then we can compare the same songs recorded on a EX upgraded unit in GS mode. But like I said, playing both GS midi's as well as GM midi's on mine before the upgrade sounded very different. Sonic Green Hills Zone theme (the GS version) sounded way off and after the upgrade, it sounded better than my SC-55's. But other GS midi's sounded pretty cool in TG300B mode, and just sounded ok after the EX upgrade. It did more than just change the name from TG300B to GS. There are different samples, effects, and instrument mappings from the original TG300B mode.
Again, I have the TG-100 and TG-300 midi modules (the TG-300 is packed up in a storage unit but I have the TG-100 right here), and can say for a fact that the sound signature of the MU2000's TG300B mode was not like its namesake as I did compare them when I got the unit in over a year ago. It is my opinion that Yamaha didn't just port the TG300 sound font from the original modules, but just tried to copy the instrument map, and use new effects and samples. That makes a world of difference in how the units sound compared to each other.
As far as the GS upgrade being closer to an SC-88 than a SC-55 I will have to take your word on that, as the best and only SC units I have are the SC-55 and SC-55 MkII. I would love to have at least an 8800 Pro or an 8820 or even a 8850. Maybe next year, then I can compare the GS mode of the MU2000EX via optical out to an upper echelon SC unit. As I only fidget with making music and never really delve into these modules, I will never fully understand how to dig out what instrument from whatever location its in. I feel real lucky when I stumble on the sound of something I like, 🤣. I mainly use them for games and midi file playback when I'm in the mood to just sit and listen to music. That being said, I may not be the best person to go to for looking into these units and trying to compare things. A real musician who understands the old modules is what is needed here.
Xenphor, congrats on winning. I thing you will like you MU90R, and you shouldn't have problems running real hardware in Linux as I know you can take advantage of USB to MIDI cables in most distros. Just find and pick a midi player and DAW and you should be good to go. I like Notation Player and Reaper, but I don't know if you can effectively run those on Linux. That Ardour looks pretty good though, you might want to give that a try.