These are what we call the 'YMMV items.' Things that some people find in this work. We call them 'your mileage might vary' because not everyone sees these things in the same way. This starts discussions in the trope lists, a thing we don't want. Please use the discussion page if you'd like to discuss any of these items.
Alternate Character Interpretation: One could easily argue the two protagonists were actually the sort of individuals who should be locked up. Considering the end result of their escape is the the destruction of an entire planet. It's later revealed in Comic Jumper, another Twisted Pixel title, that entire solar systems have disappeared. By that notion they can be viewed as Villain Protagonists.
As revealed by supplementary materials, Frank can manipulate emotions using the stone in his head. This is actually the reason he was locked up. This is also the reason the Maw doesn't just eat him. In essence Franks actively manipulating Maw to escape what may have been a fully justified imprisonment. The consequences be damned.
Esoteric Happy Ending: The game plays the ending off as Bittersweet: the parting of two unusual friends. In reality the Maw is now devouring entire planets and still growing. This implication is later confirmed in the Twisted Pixel universe as scientists in Comic Jumper have noticed solar systems disappearing with only a strange purple substance left behind. Of course, given Twisted Pixel's morbid sense of humour, this was all very much intentional.
Inferred Holocaust: The ending shows Maw devouring an entire planet. Not to mention the fact the galaxy at large now has a ever-growing planet-eating monster on the loose.