It affects loading order, which may be an issue if plugins refer to each other.
You can theoretically reorder plugins by manually renaming them in the scene JSON. Be careful to not break trigger references, though. Best way is methodical use of Search&Replace. Not a recommended procedure when you don't understand what you are doing. It's very easy to break a scene when editing JSON by hand. (TL;DR: Make sure you got at least a backup of your scene!)