My theory for the behind the scenes:

McFarland: I would like to make a star trek parody!

Fox: oh sounds awesome, lots of funny jokes and stuff. Should be funny.

M: yes haha, funny.

F: yes… Anyway here’s the money

Making episode one

M: I gotta make sure there’s loads of jokes so I can show this to execs and they see the haha bits

Making episode 3

M: okay I think they’re gone… Time to just literally make normal star trek episodes

making the last episode of s1

F: hey I see you’re almost done with the first season so I’m just checking in that the show is still funny

M: quickly adding in as many jokes as the last second as possible haha yes humor! Jokes! Plenty of them! Haha yes