It’s irrelevant how the folders in the community folder or ordered.
Important is, that the structure within that folder is not altered.
There is a root folder and in that folder are .jason files and the mod stuff.
It doesn’t matter what the root folder is named. You can rename them to your liking. As long as Community/Folder/Modfiles is maintained.
And AFAIK there is no particular order MSFS loads addons.