So.. yeah, you're not supposed to have those kinds of upgrades when fighting that one so it won't be like that in the final game.
And yep, that fight is definitely supposed to be unexpected and you already know those event triggers are a thing in this game now so there you go. ;)
I'm not gonna lie here, as this is a 100% single player game, I kinda was planning to use this save system (+- some tweaks like actually checking demo upgrades...) but I'm probably going to rewrite it a bit.
Originally, the reasons for this system were:
Very easy for me to handle and a low risk for breaking any previous saves when patching the game. (very important)
Also it's somewhat easy for anyone else to try and fix themselves if something has gone wrong. (with some guidance)
In any case, changes will be made to the system and thanks for bringing light to this issue, you're the first one who has said anything about this. ;)