The reason why the Biker Mice hate cheese is because the Plutarkians are named after kinds of cheese, so it would make sense that they would loathe a food that reminds them of a race that took over their planet.
Plus, there is the issue of No Biochemical Barriers being unlikely to be played straight and better safe then sorry.
The Plutarkians were at the head of a vast empire while the Catatonians weren't, yet the former's invasion of Mars was ultimately defeated through military power and the latter's needed a Deus ex Machina. Seems strange... 'Till you remember that the Plutarkians rely on local mercenaries for warfare beyond trench warfare and the latters are actually competent and have combined arms. The Plutarkians lost when the Rats abandoned them (they aren't shown in the flashback of the Plutarkian defeat), allowing the highly mobile yet well-armed resistance to run circles around them, overwhelm individual strongholds by concentrating there while keeping the others busy and the other tricks of a highly-mobile force against a static one, but the Catatonians were just as mobile as them while having superior firepower and air and artillery support.
Why did the Biker Mice make their home base in the Quigley Field scoreboard instead of at the Last Chance Garage? Because since Charley is their best friend and ally, the garage would've been the first place Limburger would've looked for them.
Not so much a fridge, Charley suggests them the scoreboard precisely because Limburger would never think to look for them there. Plus it's near the Last Chance Garage, so if Limburger's goons decide to attack her they're in the area.
The original series established that Lawrence Limburger wasn't the only Plutarkian agent stationed on Earth. Not only was Napoleon Brie revealed to be a Plutarkian agent stationed in Detroit, but the episodes "Diet of Worms" and "Hit the Road, Jack" reveal that there are also Plutarkian agents stationed in at least Los Angeles, Las Vegas, New Orleans, and Cleveland. What makes it worse is that these Plutarkian agents are said to be more competent than Limburger. Exactly how many Plutarkians were stationed on Earth and what were they able to get away with due to the Biker Mice not being there to stop them?
That would depend on answering a different question: how much was Limburger's reputation for incompetence owed to the Biker Mice? For all we know, these guys had limited success and only seemed more competent than Limburger because the latter had the most formidable opponents that would blow up his tower every time.
In the original series, one of the minor characters was Fourby, who eventually devoted himself to fighting back against the Pit Boss and putting an end to his slavery. While the Pit Boss makes a comeback in the 2006 series, Fourby is nowhere to be seen. What makes this worse is that the Pit Boss is shown to still be kidnapping people from the surface to enslave and the Biker Mice do nothing to stop his actions.
For all we know, Mace might have murdered a Martian mouse to usurp his identity in order to infiltrate the Martian freedom fighters in the flashbacks seen in "Once Upon a Time on Mars".
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