I wasn't - thank you for pointing that out. (I concur with your conclusion - why skip the low hanging fruit if it contributes to the single meta currency you're working towards as significantly as the harder colors do?)
Yeah, I found it strange as hell, but the worst aspect for me is that the only way to check if the color is actually complete (when playing multiple idle games) is to click Prism and see if the color you are working on is in the list. (As opposed to simply seeing the arrow to go to the next color; without the upgrade)
Still, not a major issue once you know how to handle it. If/When I reset progress (probably will for next update to check out balance changes) I will simply not purchase that upgrade for Prism because it serves little to no purpose at the current stage of development in my opinion.