When Sally and Nicole find the bomb in Bunny prosthetic and realize it couldn't possibly be from Eggman. While Robo-Robotnik was a sadistic SOB, he prefers having his legion members intact (as was the case when he saved Lien-Da life). So the risk of a bomb that would go off due to a limb shutting down and costing him a valuable pawn would be against his best interest.
As a fan realized, intentional or not, the whole story can be taken as the divide between the fans of the various Sonic continuities.
The IDW cast (Tangle, Whisper and Jewel) are coming to terms with the insanity of the Archie canon. They are also sympathetic and are willing to give the Archie cast as a chance. They are IDW fans reading the Archie canon.
Metal Sonic destroying the Death Egg leftover from Archie in response to him being treated like a disposable lackey is the equivalent of a Games/IDW purist. Someone who refuses to acknowledge the other takes on his world and character, ignoring all the good things that came to him like being his own person. (See: Shard)
The existential crisis the Archie cast (Sally, Nicole, Mina, Julie and Saffron) go through when they find out that the IDW reality is figuratively and literally paved over their own is representative of the Archie Sonic fans who had to move to IDW when the former is cancelled. They may not like it but they are willing to give this new world a chance and see if it is as good or better then their own.
The Secret Freedom Fighters along with the citizens of New Mobotropolis in contrast hate the IDW world due to it coming at their own's expense, refusing to see the IDW cast/reiterations as individuals and more of a bad fantasy. They are Pre-SGW Archie purists who refuse anything past the first or second reboots.
As for Naugus, he is more representative of the trolls who are more than happy to watch the flame wars on side. While they themselves are Pre-SGW Archie purists, they prefer making life miserable for everyone involved.
It would seem strange that Mina would run straight to Bunnie for help in the Studiopolis arc despite being shown that the latter is rebooted, has lived a life as a criminal and member of Team Hooligan. Considering Naugus was the one who spilled the beans, it is safe to assume that Mina thinks that what she heard was total nonsense to rile up the citizens. Combined with her fragile mental state at that time, it is clear that she wasn't thinking straight.
The female clothing is rather a comedic one. While female mobians wearing clothes weren't unheard of, it was rather sporadic depending on where you were from (with the 'Kingdom of Mercia' and the 'Dragon Kingdom' conservatively dressing as the norm and places like Echidnapolis/New Mobotropolis dress code being or less relaxed (Sally wearing just a vest and boots, Julie-Sue tank top with teal padding on the left side, a golden belt and large, mechanical-looking teal boots)). So finding out the whole world has a new universal dress code would certainly throw the citizens of New Mobotropolis for a loop.
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