I've figured out the problem with disappearing /tmp dir was caused by
another package (steam, from nonguix*) due to how it's packed (it
exposes /tmp dir as a guix contaner, using fhs deep in it's guts). So
disappearing /tmp dir was only caused by this one.
For now the only problem that is the core of this bug report is: if you
add /tmp file-system to yours system file-systems you won't be able to
chose "Gnome on Wayland". And as I wrote, I suppose that's due to how
x11-socket-directory-service from (gnu services desktop) works. It seems
like your system's /tmp file-system will be created AFTER this
x11-socket-directory-service will create it's own /tmp. It's mounted "on
top".
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* I don't know if it's appropriate to mention it here, I don't encourage
anyone to use nonfree software.