What I’m looking for can really be described as one of the following:
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Check out SpaceChem, matches most of your bullet points. It’s a level-based puzzle game like Opus Magnum though.
I second this, it’s what OP is asking for. Word of warning though: this game is hard as hell. It reached a point where I’d spend 2 hours on a level, realize I messed up and can’t salvage this, and gave up. I never got really far.