Can't speak to your first point, as my only interaction with Nextcloud php configuration has been to comment in/out various php modules. I don't have too many modules though, so maybe that's why I haven't had any configuration issues.

Regarding file management, the working solution for me has been to mount any external storage with a fuse mount ( NAS, dropbox, etc. ), and then just use the Nextcloud "external storage" option. Other than Nextcloud's general slowness ( I'm running on an underpowered server ) I haven't had any issues.