I just read in the late '70s version of the concordance that the the spin off show Assignment Earth was never supposed to be involved in/part of the Star Trek timeline.
The idea never sold so Roddenberry and Wallace decided to wrap it up in a Star Trek episode and see if it could then be sold. Still no takers.
As for the OP's questions, It is cannon because it was on screen and poses no great conflict with story's both before and after.
We are told Gary Seven is human, but this is never really proved. McCoy's examination could have been interfered with.
As for the time travel stuff, I get the feeling that maybe Star Fleet thought that mucking around in the past was a bad idea.
I seem to remember that an early version of the episode had the Enterprise going back in time to fight a race of time traveling aliens called Omegans bent on destroying Earth in the past.