`CustomFile` in `mem_fs` can only be read once

[Arshia001]

More context: #5374

Running mounted commands was broken because CustomFile is backed by a VirtualFile, and VirtualFile stores its offset whereas other file types are just pointers to file data. The issue was worked around in #5374, but more uses of copy_reference (which creates CustomFiles) exist and I'm not sure what other code paths are broken as a result.