He actually just made some tweets about the story, or more accurately, why there isn't one.
From what I can gather, he just couldn't think of any good story ideas and was stressing over it, and then about a month in, he decided to stop worrying about it and just focus on what he was good at instead. Pretty simple solution, but these kind of games are usually expected to have a story, so it can be hard to make that choice sometimes. I think he also said something about how he doesn't like "getting into people's heads" or something like that? Not really sure.
Also, earlier there was a update released for the Dlsite trial, but I think it only fixed like, one minor bug, so it wasn't worth dedicating an entire post to.
Oh and the endless mode was in the earlier versions from before it was uploaded to Dlsite, it basically just repeated the first two levels over and over, slowly getting more difficult, but also earning you more EXP for each kill. It was also the only way to earn money originally, doing the stages normally didn't give anything. It was unlocked after beating the two levels available, but for whatever reason the Dlsite version doesn't seem to have it available to unlock.
P.S. I screwed with Cheat Engine a little bit, and found that you can actually still play endless mode, you just have to trick the game into sending you to that room instead, I'll include a .txt file that describes the room ID's I checked and what they had behind them, though they weren't very exciting.
I don't really know how to easily explain how to use Cheat Engine, but if you know the basics, it shouldn't be too hard to figure out.
P.P.S. Pretty sure endless mode in the new version isn't actually raising the difficulty, though it's still fun to go on a rampage with all the buffs you get during it. Plus the music is cool and you can get new crystals to equip for when you level up.