Yeah, I think you either have to use their “external library” feature, which makes immich basically just an image viewer or you have to let immich handle everything but then the filesystem settings are very limited. Sadly there is nothing in between. I opted for the second option. I have the basic storage template (with folders for years, months and days) and I think that is ok by me, but I really wish I could also perma edit the photos. Fyi you can still do operations on your images on the filesystem (not renaming or moving though), you just have to refresh metadata and thumbnails for that photo (or video) in immich. I was doing that for the image or video rotations. Its still not very practical to do that, but that is at least something.