Why did the Federation soldiers have names like "Smith" and "Johnson"?
 

Read the Fugitoid and pay attention to the names. Notice anything? The people in the federation have names like Fredericks, Smith and Johnson. Kind of odd names for aliens, wouldn't you say?

I know the Fugitoid wasn't originally meant to have anything to do with TMNT, and that production of the issue started before TMNT. So I would have just said the alien status of these characters was a simple retcon, but it was never published before TMNT. In fact, it was published after the fourth issue of TMNT, with the TMNT at the end. Meaning Kevin and Peter could have gone in and changed the names before print.

Was this oddity ever adressed?

I mentally assume that since they can't be speaking English, we are getting a Universal Translator equivalent of their dialogue. And names.

Their real names are probably just homophones for the given names by the comic.

Why do people in Star Wars have names like Ben and Luke?

Made up galaxy in a universe seemingly without earth or the milky way, so nobody cares. High Fantasy rules apply there. Like how you can't find Mordor, Skyrim, Westeros, Prydain or the Earth Kingdom on a real world map yet the stories you find them in still has some recognisable real world elements, like names.

The issue here is that earth does exist in TMNT, which makes you question what the connection between earth and the federation is. And it's not like Dragon Ball where the planet is called earth but can basically be described as "Ancient China with the cites and vehicles from the Jetsons, with the home appliances being on the technological level of the 80's, 1/3 of the people are anthropomorphic animals and dinosaurs roam freely", it's not that screwy. TMNT kind of falls somewhere between Harry Potter's world (craziness exists all over but it's virtually unknown amongst the populus) and the Marvel Universe (craziness is everywhere and is public but contained within the framework of the real world).

And it's literally called "The Human Federation." Yet... they're not human?

Maybe Earth was colonized by the early members of the Human Federation as a social experiment or something.

Come to think of it, isn't it odd how the turtles were teleported directly from earth to a planet populated by these not-humans? Maybe D'Hoonib is the place Utroms zapped nosy humans for 20+ years?

That sounds like a good theory.

But in 20 years these exiled humans were able to assemble and organize a whole Human Federation, with ships and spacecraft and a complex military and advanced tech?

Two ideas:

1. Time Dilation. Remember how on earth, only a few hours passed while the Turtles were obviously gone for way longer? In the 4Kids cartoon I think it was 8 hours on earth and 5 weeks for the turtles. Assuming that's true for Mirage as well: 5 weeks is 840 hours, meaning that 105 hours pass on D'Hoonib for every hour on earth.
2. Hijacking. Seeing how that sector of space was full of advanced aliens, it's not unlikely they could have stolen tech or bases from a native or visiting species.

That's assuming a lot. The whole space odyssey in Mirage wasn't much more than a few hours, maybe 12 at most before they reappeared in the bathroom on Earth.

Do you mean 12 hours on earth? In that case you're wrong. I went back to check and on the very first page of issue 7, you can clearly see the reporter saying it's been 3 days since TCRI emitted a light beam.

If you mean it's been 12 hours on D'Hoonib, then time would pass 6 times faster on Earth.

Even if it's indeed the case, I seriously doubt 12 hours really makes sense. Granted, it takes place in space and nobody says how long it takes, so I can see how the time duration is up for interpretation. Even so, thinking about all they do and the things that have to happen between the panels, I don't think it all happened within a few hours. Advanced spaceships or not, I don't think you get from D'Hoonib to Triceraton space that fast. To me, it either happened within the same 3 day time span as on Earth or longer.

Star Wars takes place in another galaxy but the same universe/reality as our own. Complete coincidence maybe? There are literally so many planets with life on them that there have to be at least two where humans and human language evolved the same way?

Wouldn't the 2003 show have to take place in the same universe as Star Wars since Han and Chewbacca are present?

Because they couldn't think beyond war = American Civil War of 1861–1865. :)