Well, the tip partially works, I figured it out, and it doesn't work for the reasons I thought it worked. It's because the files are in different paths but still being parsed, if the files are identical in path to any other omd installed you'll still end up with a conflict.
So, for example, instead of needing a merge folder, name your MERCHANT_GENERAL_INVENTORY.DAT file something unique, but leave the name string inside the file the same.
If your mod is RespecPotion, for example. Name it MGI_RespecPotion.DAT it'll load and not conflict with other addons.