Full disclosure: I only read I Am Slaughter from The Beast, so I took your characterization of Kalkator, and the book quotes, completely at face value. So it may be there's some context here that you assumed I'd know that should change my perspective.
The basis for my assertion vv "retarded gobbledygook": the basic underpinning metaphysical assertion for 40K is that there is no God. Which is to say, there is no omnipotent, omniscient, Prime Mover which created and sustains all material reality by the force of His will, and whose nature and attributes define the standards of truth, morality and goodness. Instead there are many gods; that is, immensely powerful beings and cosmic forces which are able to exert tremendous influence on reality (physical and spiritual) and which claim a large base of sentient adherence (usually, worship). These gods represent durable but ultimately transient metaphysical realities, and have in both theory and fact changed over the epochs. So for the Eldar gods, the Chaos gods, Gork and Mork, the Old Ones, the C'Tan, the Greater Good, the Emperor etc.
I understand that the majority of the Imperium no longer understands or believes this, but we as the readers know they're ultimately wrong. And fortunately, the argument between Kalkator and Bohemond is between two people who are fundamentally In On It metaphysically. That is, they understand the aforementioned assertions to be true. So in this particular case we don't have to worry about that additional perspective. It's "in the game" (Magneric and Zerberyn), but it's ultimately meaningless in this scenario. It's a foil, nothing more.
It seems to me then, where there is no ultimate Standard by which all other reality is defined and against which it is judged, everything very quickly comes down to brutal pragmatism, both immediate and future. "What's in it for me? What's in it for my people? What's in it for my race/nation?", and so on. The question is no longer to find an ultimate reality to which you adhere. It is to decide what god best serves your, or your group's, interests. Or indeed if you yourself are the best vehicle for those interests, rather then some nebulous deity or ideal. In this sense, the supposed hypocrisies, the past lies and so forth of the Crudade-era Imperium, are dross in the argument. They are rhetorical flourishes, and shoddy ones at that. This part is what I was aiming at with the whole gobbledygook stuff. If the Emperor lied- if he built a mountain of lies, if he dealt in manipulation and dastardly deeds and so forth- my fundamental immediate retort would be "who gives a fuck?". The question of real import is: does the Emperor have the will to power to make the universe bend to his will, as any other god worth the name in the 40K universe does? The answer is yes. In that sense he is worthy of "worship", even if it's hollow. Following from that central question I would then need to decide: is the Emperor worthy of MY worship? Does aligning with him serve some interest of mine, whether physical or spiritual? And, just as important- if not the Emperor, who? Another god? Chaos? Myself? ...another Space Marine?
A large part of the reason I sneered at the quoted exchanges was due to the way you originally characterized Kalkator:
...making his little empire with people worshipping the IWs as gods (i.e. tyranny without too much grimderp and without Chaos fuckery).
Taken at face value that just makes Kalkator the Emperor, but smaller, meaner of spirit, with less power and reach, and with no discernable improvement in station for his subjects. He's trying to be the Emperor without any of the very real power, intelligence and wisdom the Emperor himself possessed. It's a losing proposition all around for any would-be adherent. At least the Emperor, target of the wrath of all 4 Chaos gods, isolated and alone, for all intents and purposes a revenant, can still stand toe to toe with them. Same with the gods of Chaos. Kalkator? He's shit on any other god's bootheel. Why the fuck would he be deserving of me going turncoat? What would the point be? Some principle or other? Laughable. I'm just switching one monumental liar for another, only now with less power behind him.
And your added context (sneaky bastard!):
...that they should rule over humanity since they represent a superior version of it (and that they should be worshipped not as gods, but as the pinnacle of humanity which they represent).
Only makes it a more silly proposition on its face. So he's not even claiming to be on the level of the Emperor, but he thinks others should give him the same level of adherence?! It makes even less sense now. By that logic he should still be "worshipping" his Primarch, and Pert should have stayed loyal to the Emperor!
All of my blather of which I tried to sum up in my one-liner:
"I'm already serving one proclaimed living god, why should I switch to serving another who is demonstrably less potent, with precisely the same contempt for the truth (what truth there is in the Warhammer universe) by his own words, and who displays demonstrably more contempt for the welfare and future of his servants?"
And again, it's not so much that it's unreasonable to suppose Bohemond would still have made the decision he did given all of this. People do such foolish things all the time, using the flimsiest of self-justifications as pretext. It's that he didn't even bother asking the question. It drives me nuts. In the entirety of the 40K library I can only think of three times it's been pondered in these terms: Alpharius dividing his allegiance between the Emperor and the Cabal, Lorgar deciding that the gods of Chaos were more worthy of worship than the Emperor (based exactly on what I said above, by the by: "what's in it for me/for humanity?"), and Guilliman pondering the Emperor's godhood in the Dark Imperium trilogy.
Anyways, thanks for giving me an excuse to vomit this out. I've been wanting to talk or write out my thoughts on the metaphysics of 40K for ages :D