Only issue is they’re stored in my server as belonging to the server user (I assume everything in those directories should belong to root and I can just use chown?) But I also don’t know if they retain the same permissions when backed up.
Not everything will be owned by root, and some of the binaries will be setuid or setgid, some might even have extended attributes (e.g. ping will usually have a security.capability attribute). /var will also have a lot of different owners.