I have been using EB's Bakery and EB's Windmill mods as standalone mods, and they are still being flagged red? However, in the game, wheat is being converted to flour, which in turn into bread with no problems. Am I missing something?
no, mods turn red cause some files are named the same and some different. nowadays most mods do show red. long as they work and have no issues just ignore that.
The red only means that more than one mod is accessing the same game code. It's fine.