Well, prerequisites and costs are different features, and mods can mix and match them however they want. You could make it so the rocket silo takes only red science, and space science require blue, purple, and yellow only if you wanted. This mod doesn't change the actual research progression of the game, it only cleans up the tech tree for when multiple mods adding or changing techs are involved, and makes it so the only yellow "researchable" techs are the ones you can actually research, like the examples in the mod gallery page. In vanilla, the tech tree happens to be made so you never have techs that require less packs than their prerequisites, like your example.
There's not a good way to algorithmically restructure the tech tree to make the tech pack order like vanilla while also guaranteeing it doesn't break progression in some way, even if that was something the mod was supposed to do. Maybe electric trains was adding their tech after another mod was, which might have messed up the pack requirements, or maybe that's just the way that wanted to do it, I don't know. Point is, this mod isn't supposed to solve the issue you're having. Sorry, I wish I could help more.
