There were once humans, but...[]
In the final days of humanity, human DNA was being combined with cats to create a race that could pick up where humans left off. Of course, humans would be prehistoric to the kats. And ironically, most of the villains are distant descendants of Ted Turner. (Actually, they're on another planet entirely. The original plan for "When Strikes Mutilor" had the aliens who originally owned the ship wearing spacesuits all the time, because Mutilor altered the atmosphere within the ship to be toxic to them. After the Swat Kats left, they would've re-stabilized the air supply and removed their helmets to reveal themselves to be humans.)
The series is the ultimate end result of the Ace Combat Universe[]
The Turbo Kat easily rivals - if not surpasses - many of AC's superplanes such as the Wyvern and possibly even Falken. T-Bone and Razor might have gotten the idea from archeological digs that brought up centuries-old fighters, one of which was fittingly the F-14 Tomcat. How do they find out about this stuff? Their version of the internet, of course. How the Kats come to replace Humans on Strangereal is anyone's guess, though. Perhaps some of the Monsters-of-the-week can actually be traced back to "ancient" weapons from AC's world. This also means that there could be a city-state (as per an above WMG) trying to build and perfect an airborne fortress akin to Gleipnir, or an uberfighter that rivals the Fenrir (or rather is Fenrir).
T-Bone remained partially mutated after "Mutation City"[]
Even though most of the physical signs of his being a mutated frog-kat vanished, the anti-mutagens couldn't restore him entirely to normal. That's how T-Bone managed to swim at the end of the episode when he sank like a rock every other time in the water: he's still partially a frog. It's also how he managed to get to Razor so fast: heightened senses and increased speed and stamina.
The Dark Swat Kats are also disgraced Enforcers.[]
After Feral ruins their careers like the mainstream Feral did to the protagonists, they also figured out they could use spare parts dumped at the junk yard. Unlike their counterparts from the main dimension, they let their hatred of Feral overpower their desire to stop bad guys and it led them to a Face-Heal Turn.
Feral knows who the Swat Kats are, he just pretends not to, to give himself some plausible-deniability, since they can get away with stuff he can't.[]
In fact, Feral not only knows the truth, but he created the Swat Kats on purpose. Let's go back to the beginning when Jake and Chance were in the Enforcers. They were the best pilot/gunner team Feral had. However, Feral runs the enforcers in a very by-the-book manner, and it's probably held them back on more than one occasion. Then Dark Kat shows up, and in a totally uncharacteristic moment of glory-hogging (he usually denies to admit the Swat Kats helped with the villian of the week, but I never saw him act that way in combat), he bumps their jet (despite Feral himself being an excellent pilot) and knocks them into the Enforcers' Headquarters.Now he probably didn't intend that much damage, but it accomplished his goal. Now you've got two people who owe several million dollars to fix the building. Why would you send them to a scrap yard, completely unsupervised, to work off their debt? Because Feral knew they wouldn't be able to just stand by and do nothing, and he also knows just what kind of scrap ends up in that yard.Fast forward to the present. Feral always complains about their vigilantism, but he has never once fired on the Turbokat while the Swat Kats were at the helm (alternate universe excepted). He also didn't seem too convinced when Hard Drive as T-Bone threatened the city in exchange for money. It's as if his pursuit of them to "uncover their identities" is just an act - a means of keeping them on their toes, perhaps?Not only that, but the technology in Megakat City is absurdly advanced. I find it hard to believe that Feral is never able to track them back to the junkyard hangar. Even if there was a jamming system in place, the junkyard is the only thing out that far in that direction. Just watching which way the Turbokat flies a few times would clue him in.Then comes Felina, the niece that he's super protective of. He's pretty much always with her except for when she sneaks off, but he doesn't put up too much of a fuss when she goes with the Swat Kats.Finally, let's not forget when the Metallikats learned the secret identities and offered them to Feral. He could've gotten the info from them and still arrested them, or have Dr. Hackle get the info from their computerized brains manually. But no, he neuralyzed them, making sure no one would know their identities.So why did he do it? He knows that as the law there's only so much he can do, so he put the best team he had in a position to work on their own. He also arranges for a bunch of high tech goodies to wind up at the junkyard without being decommissioned (missiles, etc.) to keep them in business.