I know this is an old thread, but I just wanted to add that I commonly run into this issue and wish there was a way to merge evil twin directories that have different contents.
I most often run into this when I am ramping up a remote unity contractor, say for instance an audio engineer, and I want them to be able to add their content in an isolated branch without needing them to sync the entire project contents. That in itself would be fine, however a lot of those cases there are a number of third party tools from the asset store that contractor may need. Importing those tools from the asset store to their branch often creates a number of the standard unity directories, plugins, gizmos, ect which of course are already in the core project and causes this merge issue down the line.
