No, your logic is not flawed. Unfortunately, the law can be quite illogical about these sorts of things. Derivative Works violations will be construed every time you modify another modder's objects directly or indirectly either at compile-time or at run-time. The user has no say in the matter (aside from not using the mod, but that's beside the point). Fair Use cannot be claimed, because that only applies to referencing someone else's work for the purposes of advertisemant, education, or criticism. Once you touch someone else's work, you infringe on their intellectual property. If you created the script that was designed to perform the changes, you are the person at fault.
Mods that use global scripts that do not discriminate towards particular mods are within Fair Use, so Bash and SkyProc are fine.
Well yes, so my point was that eventually, with relative ease and some creativity you arrive at the point where the intention to target a specific mod is no longer given, yet it achieves the same effect.
And another thing to consider:
If I make a masterless patch, that is NOT based on another mod. It's a standalone work that runs even if the other mod is not present at all. It may have an effect on it - that effect may be all it's good for in the end. But it does not contain data from the other mod, and technically it's not based on the other mod.