/devil's advocate
I agree with your reasoning, but I think it is good to mention that in my humble opinion you are only trying to find rational reasonings where it can also be something very different too. For example, I am not even sure that the Amarr are homophobic because of their religion (Maybe ? I don't remember the chrons). We just assume they are because RL monotheistic religions are against it. But maybe instead it is just about traditions ? Like the Voluval exiles ? Something that does not make any sense but is still here either by ignorance, or sheer stupidity of the masses. Such cases are legion RL too.
This is precisely why I expect that the Amarr don't have much, if anything, against it. What would be the justification for it beyond religious reasons? The Amarr are the biggest of the four Empires. To continue in the earlier vein, there's no population issue to speak of, so people pairing off in "unorthodox" ways hardly causes a problem there where such policies might be "needed."
While I could see it perhaps not being too common for people in positions of relative power (Holders, Heirs, etc.) to be in or open about such a relationship, as long as it's not being flaunted or rubbed in people's faces (ie, keep PDA to a minimum; holding hands in public is okay, making out in the town square not so much), I doubt there's actually anything against it. So the local Holder prefers a firm rod of human flesh up his tailpipe instead of the standard-issue Amarrian Stick. As long as it doesn't interfere with his duties as a Holder or disrupt the lives of his underlings, why should it matter to anyone else?
Of course, if it actually became a problem, I'd wager it's safe to assume that in those situations traditional Holder politics would resolve the issue in one way or another.