I’ve taken pictures with the lid on and it looks like this:
Red gain 2.75, blue gain 1.8, exposure 4000.
Looks much more uniform, so I’d wager the light source (or there being light in general) does have a play in this.
@PM490: The explanation of your findings goes a bit over my head, unfortunately. Aside from programinng, I don’t have any true expertise or education in any of the subjects useful for creating a film scanner. I’m just tinkering and trying my best at learning as I go. Do you have any resource that could help me better understand what’s going on, or maybe, like, an ELI5 version? 
If it takes up too much time, please decline. I appreciate your (and all the other members’) contributions very much.
(night - Why is it that when the green channel clips, it turns into blue? - Photography Stack Exchange this was helpful, for starters)