Oh wow, I know exactly which minigame you were talking about when describing what inspired the brewing puzzles. I even own a physical copy of that Mario Party game.
(In fact, I used a very similar puzzle in an old unpublished game of mine, but made it extra confusing by having the words that describe which colours to pick appear coloured in with different colours themselves.)
That one scene right after the battle with Solik is the one instance where, at least in my personal interpretation, it becomes very clear that even Stoic as we know him now is far from a perfect person. Of course, all of the characters in Master of the Wind have flaws, make mistakes and sometimes do morally questionable things. But this is the point where I always felt like even considering the context, Stoic's actions are extreme and borderline evil. Which of course puts the fact into perspective even more that his hundreds of years of experience have helped him understand the world in a certain way, but didn't leave him less emotionally vulnerable. And while that's quite sad, I think it's also a good choice to create some distance between the player and Stoic sometimes, as is likely to happen in this scene.
Solik's character, the Midnight Guild as well as the workings of undead in Solest in general definitely are a welcome shift away from classic depictions of necromancy, and definitely made me question why by default it's so often automatically considered a wholly evil and unnatural practice in the fantasy genre. I really hope to see more explorations of this kind in the future.
And you were right, I had never found that secret you need to go back into the lab for. In fact, the idea never even crossed my mind, despite the closed door that was right there. And here I thought I knew this game pretty well. Thanks for sharing that bit!