You are missing the point.
You can make fun of everything. You can jam in jokes anywhere.
Hell... just put a laugh track on it and some people will laugh at anything.
Just like with that show where people tune in to laugh at how awkward nerds are.
You can also parody SciFi up the kazoo. Most of it has already been done by Red Dwarf though.
The fact that there is room for jokes can't change the fact that Galaxy Quest was not about joking about SciFi tropes or making fun of such shows or its audiences.
That's what The Big Bang Theory is about.
Galaxy Quest is your classic "the dream is real and I am secretly a hero king" story.
And THAT story can't be stretched out for too long before it becomes a genuine story of heroics and NOT a parody.
Galaxy Quest ends by becoming Galaxy Quest the Journey Continues.
It stops treating the show or the work of those actors on the show as a joke - but as a real and highly important MISSION.
They are no longer actors. They are an ACTUAL HEROIC CREW of NSEA Protector which was a real starship.
They are no longer acting. They are on a diplomatic mission, sending messages into outer space.
They have a real living alien with them on the set. They KNOW things and they did things that have changed them and the entire universe they live in.
The ending changes the GENRE for the audience. It becomes obvious that it is not a SciFi parody but genuine SciFi.
Because it is a love letter - not a parody. Goofy characters become heroes.
Seen Guardians of the Galaxy?
MASH never stopped being a comedy, turning around and making every joke actually just a bizarre scene in a gritty war drama. If it did, it would be Kafkian.
Neither did Hogan's Heroes.
Nor did Lost in Space or Star Trek get a laugh track and started being about crazy hijinks of a wacky crew.
They can try doing that, sure, but all they'll end up with is just another lame "reference is a joke" show, like that crap Seth MacFarlane keeps churning out.