something that is very interesting rereading early MTMTE is that the comic is actually very much written with the assumption a ton of its readership are specifically pre-existing IDW comics readers, which can sometimes be difficult to remember because of the fact that a lot of people wound up coming onboard to MTMTE from outside the fandom in the end and now it has a reputation as an entry point as a result. this manifests in a couple ways throughout the first couple major arcs. one obvious one is that the Overlord stuff functionally makes it a sequel of sorts to Last Stand of the Wreckers, at a time no direct sequel was planned. but my favourite is that there's a kind of narrative trick the comic pulls with the leadup to the payoff Remain in Light gives us for Magnus.
the Magnus we get in early MTMTE is not the Magnus we get in earlier IDW comics. he's very exaggerated; where phase one Magnus is a by-the-books stickler for not so much as bending rules and someone we see struggling to maintain that sense of moral uprightness in the face of the war and the people around him being far less dedicated to staying on the straight and narrow like him, it's completely turned up to eleven in early MTMTE. phase one Magnus would not be doing endless doorframe audits, or throwing people in the literal brig for crooked badges. but this doesn't necessarily register as a change in character so much as a change in genre. MTMTE is also a dramedy with heavy emphasis on the comedy side of that in a way no other IDW comic is, and the shift in Magnus' characterisation therefore feels like 'well in THIS genre, that's what that archetype is like', rather than a diagetic shift in character. even if you come to MTMTE straight off those prior comics, it is very much a 'roll with the genre shift' thing rather than a 'hm. Magnus is acting… weird' thing. you let it go.
there are a couple indications this might not be the case early on. Rodimus especially seems to be under the impression that Magnus is acting uptight even for him, with his insistence on waving it off like 'he needs to relax, Swerve can you get him to chill on Hedonia because my guy is REAL stressed' and the like. (this makes sense- Rodimus is the person on the ship who has actually been directly interacting with Magnus regularly pre-MTMTE.) but it's not super obvious and not heavily emphasised.
which makes the eventual post-Overlord and RiL reveal, which is that Magnus has in fact been acting weird because he's having a breakdown that has largely gone unremarked upon by his shipmates, really really good. Magnus has not been doing doorframe audits because he's the comically uptight second in command acting as straight man for genre purposes; Magnus has been sending Rodimus a million memos a day and losing his shit over nothing because as someone whose entire identity as 'Magnus' is rooted in a wartime role he escaped into, he's been having an existential crisis now the war is over and he has no purpose and doesn't know what to do because he never expected to have to play that part in peacetime. the entire time the genre shift was somewhat obfuscating the fact this characterisation was a thing that is in-universe relevant, which also then reflects back on the fact Rodimus is like. hm. probably should have noticed that, now I feel like an asshole for not realising. (the scene where he and Rung discuss those unread memos, post-Overlord.)
it's a small thing, but it's a really effective misdirect for the payoff Magnus gets in RiL that reads a hell of a lot more clearly on reread and rewards that chance to revisit the early issues with that knowledge. of course that wasn't just a gag, of course he's actually slowly losing his shit slightly, he cannot go five seconds without making it clear he is Stressed As Hell. but until you get to that actual reveal, there's just enough room for the comic to let a reader assume it's, you know, we're in a comedy now, we need a hilarious straight man, and Magnus is it. it's great! all the stuff MTMTE pulls to simultaneously obfuscate the Magnus/Minimus reveal while also making it feel completely reasonable on reread is great. really good use of reader bias there.