I'm not sure what your expected result is? If the system does not have a fqdn, which is very common, especially with many SOHO users, then what should it be set to if not hostname?
I do remember years ago when lots of systems assumed/expected a fqdn. To make things work correctly, you had to define localhost.localdomain as many systems use a test along the lines of "has at least 2 components in the domain name".
My current home machine, with a pretty much default Ubuntu setup has a hostname of tim-desktop. If I use hostname -f it is still tim-desktop because this machine does not have a fqdn - I don't have a real domain name, so cannot have a real fqdn. If I did, the system would be configured accordingly and hostname -f wold return the fqdn.
Is your concern that even when you have a system setup with a fqdn that emacs is still only using the hostname part i.e. not hostname -f? If so, yes, this is probably incorrect.
On the other hand, if you are concerned about the fact that if the system does not have a fqdn, you don't get a 'real' email address (or at least one which looks real, but may have no MX)? If so, I don't think this is something emacs can really do much about and at least an obvious 'bad address' is better as it may alert the user to the problem.
Yes, this does mean that when you do emacs -Q on a system without a fqdn, and then try to send a bug report, the address is incorrect, but that is probably the least of your problems. The email is unlikely to be sent as the system is unlikely to have a correctly configure MTA. If it does, it probably should be configured to re-write the from address to be whatever mailhob/smarthost the system uses anyway.
I recall a number of threads in the past about this issue and suggestions to do things like change bug reporting to use a web service instead of relying on email. However, most of these alternative solutions either added additional complexity or required additional infrastructure which someone would have to maintain. From memory, managing the additional infrastructure to provide a web service for bug reports and ensuring it was secure and not susceptible to spam/abuse was the real issue.
At the end of the day, I don't think being able to send email correctly from emacs -Q is anything Emacs can reliably solve. However, it isn't a big issue - I've found it pretty easy to just select the message, copy it into my mail client and send it that way. From memory, I think there is even some text in the bug report template warning about this and what to do.