Well, had a meeting with them(TKO Soft was a team of two brothers who made doujin, one doing the programming and one who made the art), here's the information that I was able to figure out.
Alpha DOS - I wasn't able to find anything out about this, sorry.
Early Games - The bulk of their PC88 games were simple RPG or Adventure games using whatever engine they made for Jark(Ryu system). They have physical copies of them somewhere, but they haven't dumped the images.
Graphics formats - The formats for the PC88 are a custom format that the programmer made himself. He programmed his own graphics tool in BASIC and used that to make the images. I assume that this was the standard practice for creating graphics on old Japanese computers. I believe that the PC98 graphics were hand-drawn and then scanned, but I wasn't quite sure if that's what they said. I don't know if the PC98 games had a custom format or not.
General History - I wasn't really able to get a "why" or any big names, their involvement in the scene started around 1988. They would usually sell their games at Comiket. The PC88 and 98 doujin were able to become the most well-known because those systems were the dominant ones in businesses. They didn't make anything for any other computer systems, but they held the X68000 in very high regard. Due to its strong power, but high cost; it was a bit of a distant dream for computer-users.
Other Things
- The story for the first Yugekitai game was based off of a short film that the younger brother made with his high school classmates. As such, the games characters are based off of his real classmates, but with the names slightly changed.
- The original disk version of Yugekitai II originally took up 10 disks, fortunately it's possible to run the game from an HDI.