The Top-Folder name of an MOD seems to be of no relevance other than the loading order. I am constantly renaming Mod-Folders without changing layout.json or anything else and it is working.
Same here. It’s fine to rename the top level. I rename mine to keep things organized better.
However, in prior patches, MSFS seemed to take care in rebuilding the Content.xml file after I deleted it (similar to how X-plane did it). But in the latest update, the Content.xml is just sorted alphabetically. I wonder if this will change or solve any scenery issues??