Engineer is noticeably out of focus in the comics, and there are two important throughlines in his characterization contributing to this.
The first is that out of the nine mercenaries he's always been the most plugged in to the backstory- the comic where we learned his real name is the one that introduced the backstory, he's the only one of the mercenaries to have actually canonically met one the Mann brothers, the only one who for sure knows what the gravel wars are ostensibly being fought over- and that level of involvement with the background plot, coupled with his genius, level-headedness and comparatively high empathy, makes him difficult to position front-and-center as a protagonist without breaking a bunch of things.
The second thing setting him apart from the rest of the mercenaries is that while he's enough of an eccentric to rise to the challenge of the setting's gonzo insanity, he's almost never the instigator of any of it. His Meet the Team video consists of him sitting and relaxing while his sentry guns mow down waves of assailants, monologuing about the measured practicality of his escalating response. His response to the teleporter tumor problem in Expiration Date is a grounded and practical approach to a ridiculous situation (that's exacerbated by Soldier.) He's minding his own business when a rocket full of space guns lands on his back acre on Christmas Eve, he spends the entirety of Loose Canon flummoxed by Blutarch's amoral insanity (though importantly, he's nonetheless willing to take the man's money for services rendered.) He's a fantastic straight man when the narrative needs such a figure, but his isn't a flashy insanity. He's not Soldier, he's not Medic, he's not even Heavy as far as out-of-pocket gag behavior goes. Almost all humor involving the Engineer has to do with his reaction (or lack thereof) to the bizarre carnage around him.
These factors are reflected in the role he ends up playing in TF comics 6 and 7. He's kept in the background of the plot in a reactive role, doing his professional best as an Engineer to maintain the Administrator's life extender- a frustated care-provider to a deeply unwell patient who doesn't always take his advice, a grounded, practical facilitator of what ultimately turns out to be the most deranged behavior of the entire story, seeing his contract out to the bitter end. And this is the way in which his apparent groundedness wraps back around into a distinct brand of crazy, no better than anyone else. The Administrator's real plan is something he's a reasonable enough person to disapprove of in the abstract. He's clearly aware something is rotten at the core of all this- he describes Miss Pauling actually managing to recover more Australium as her having created a problem rather than having solved one, he was on some level relieved to realize this was all drawing to a close. But none of this was something he was willing to break his professional obligations over and thus something he (and two generations of his family before him) deliberately kept themselves in the dark about so that they wouldn't have to reckon with it or make that call.
This passivity and level-headedness allow him to play an extremely important narrative role once everything is out in the open- he's the only member of the main cast who can present Miss Pauling with her Road-to-Damascus moment over what to do with the remaining Australium with any credible gravity. He's the only character left in the main cast besides Pauling herself who's plugged in enough that his analysis of her situation carries any weight. He's the only one of the Mercenaries from whom "If you keep it, I won't help you" means anything at all or is even a believable ultimatum- the rest of the mercs might have been freaked out by The Administrator specifically, but do you really think they wouldn't have just kept following their friend Miss Pauling if she kept signing their checks? He does what he's always done- he examines the situation, lays out the available options, and leaves the final call up to others. The only thing that changes- and, to some extent, a sign of his off-screen character development- is this time is that he finally draws a line in the sand as to what course of action he'll lend his expertise to. He threatens to finally, finally remove himself from the situation unless Pauling decides that she wants him to help her finally, finally solve the problem once and for all.