I'm having the auto-purge issue as well. I narrowed it down to an ENB that I'd flagged as such, but it had Data/skse/plugin/ files as well, so it had a Data folder included. It shows the ! in the Dependencies column like it does when you individually override one of the file conflicts, even though I wasn't doing so on this mod.
I'm also a bit off label in my usage. I zip the SkyrimSE game binaies and Data contents up and deploy each as a separate mod, but those don't seem to trigger whatever is going on.
I'd like to vote on killing this auto-purge feature with fire. Just give me a warning instead.
Vortex.zip