Yes, system users tend to not have a home directory. But you are fully able to create one for a new system user if this is what you want to do.
You are also able to create all kinds of temporary directories and read-only filesystems for a process (e.g. using systemd) if this is what you want do to.
Yes there is a lot of fragmentation and no real standard, which is a little disappointing, but you sure have options to work with. And these options do not have to involve any legacy-ish filesystem components like /var/tmp that nobody knows the purpose of.