So I've been glancing around at these craft mods for TFTD, and I noticed most everyone seems to be convinced that the sleeker, wider part is the 'rear' of the hybrid craft, like the Hammerhead. I'm not so convinced - in fact, I'm quite certain that parts of the game where orientation is consistent, such as the sprites used in the base view (which consistently have crafts facing downward in the sub pens and equip sub screens) and the interception window (where the damage displays consistently have the crafts facing upwards, towards the hostile USO), clearly indicate that the wider sections of these hybrid craft with the sloped 'wings' are, in fact, the fronts, making their battlescape layouts reversed from how the Triton is oriented.
One of those visuals that has stuck with me from this game is that of the Hammerhead Ufopaedia entry, which, to me, always looked like the Hammerhead about to dive into the water, firing its single hardpoint, and not, in fact, the craft breaching the water with an engine trail, which just doesn't seem right at all with how propulsion appears to be depicted in this game, especially without any sort of 'splash' effect with the water where it should have exited. The only disturbance of the water I can see by the Hammerhead in the artwork appears to be a bit of water splashing up onto the right wing, possibly from a wave just clipped as the first sign of re-entry into the seas or seaspray thrown up just enough to make contact and streak up the wing.
This is also consistent with how the USOs are designed. Generally-speaking, the rear is the thinnest part, while the widest section, generally where the main entry point is also located (on the USOs, at least), is the front. This is supported the fact that, consistently, these thinner 'rear' sections tend to be where the Ion-Beam Accelerators and Zrbite storage are housed, and the wider sections tend to be where components that look more like control consoles are located. If X-COM scientists and engineers were to emulate these designs, they would be doing the same thing- making a wider front with a thinner rear (albeit placing the entry points either at the rear or close to it, more in line with the older human designs).
This is just further evidence supporting my perspective that the Hammerhead's exit, and the Leviathan's seeming 'view slits', are, in fact, in the rear of the crafts, and, in classic X-COM fashion, we have no access to the pilot's cabin or cockpit in tactical battle. In fact, we can't even see it, as it's inside the center of the sloped sections, with no cutaway.
What I'm getting at here is... The Ion-Beam Accelerators are at the wrong end of the troop compartment. If you really want to have them in the layout, either keep them along the outer walls, next to the 'wings' (I would have just assumed they were mounted inside the 'wings', anyway- the Hammerhead's battlescape layout certainly gives me the impression of a drive system in the visible wing edge) or try to stick them closer to the actual rear, not right behind the pilot's head.
I realize I'm over two years late with this comment, but oh well. And I'll also note I understand why this confusion's been around for so long- these ships' orientation in the battlescape is completely reverse of everything else before them- the Skyranger, Avenger, and Triton all faced southward when landed, so why would the Hammerhead and Leviathan be any different? But the visual cues are there in every other detail in the game.