Not quite. So, in the original release, everything was just vanilla weapons. (Well, some of them were altered by BP, but you know what I mean.) This included green Prom Rs, as the starting weapon. When I started modifying assets to make them more HoL-appropriate, I eventually decided to create variants of all the weapons that didn't have red, orange, or yellow effects. (Well, except the Akheton, but nobody cares about the Akheton and it's never really used in the campaign. Also I forgot it existed.)
So I made a Hammer of Light variant of the Prom R, which shoots red bolts. You are supposed to be, by default, equipped with this red Prom R in all of the first seven missions of the campaign -- up until you
retrieve the supplies containing Mekhus from the Revelation and Witness in Mission 7, "The Bitter Scroll".
Now, in the version I released last month, I left the original, non-HoL variants of all those weapons -- including the green Prom R -- as options in the mission loadouts. I figured giving the player extra options couldn't be a bad thing. In retrospect, this was a stupid decision -- it just creates pointless confusion, especially since I'm not even sure it's possible to tell the variants apart in the weapon select screen.
So, in the version that I uploaded (or at least tried to upload) a couple days ago, I fixed that -- the mission loadout options only give you access to HoL variants.
But for some reason the version you guys are getting is different from the version I uploaded. (Both times. Borked loadouts involving Akhetons were never part of anything I uploaded.) It sounds like what's happening is that my HoL weapon variants are missing from the mission loadouts for some reason, which is why they only appear in the red-alert missions -- in those cases they're forced in by the mission's red-alert status. As for why they'd be substituted with Akhetons...my guess would be that it's because you're required to have at least one primary weapon, and...maybe the Akheton comes first alphabetically...?
Based on some other things Mito said, I think what might be going on is that the game is using old mission files, from the original release. (But maybe only partially, or something? If the old missions are being used, the weapon variants shouldn't be present in the red-alerts, either. It kind of sounds like the game is trying to mash the two versions of the missions together, but I don't know how or why that would happen.)
For reference, could you guys tell me some other things about the missions you're getting? Specifically, what color are things? All of the HoL ships, from warships to fighters (with the exception of the Bes-class Witness), are supposed to have red glows, rather than the original blue. Which are you seeing? If they're red, are all of the ships red, or is it just the Typhon and Aten, with the others still being blue?
Similarly, what do the blobs from the HoL's turrets look like? They're supposed to start yellow and gradually turn red, as well as having a slightly different texture from the standard blobs. Do they look like that, or do they look like the normal ones? (Or are they starting-yellow-turning-red, but still using the regular textures -- the way they look in the OP's second screenshot? I ask because the different texture was a very late addition, so if you're seeing an intermediate version that might shed light on what's happening.)
I really do apologize for how much a ****show this is. Unfortunately I'm genuinely not sure what's going on here or how to fix it.