Good day Mr. Reaver, it's a been a bit since we've last talked but considering your recent update I'd like to explain what I believe to be the issue with automatic weapons.
In order to make aliens stronger and the game more fun and challenging you have made enemies far more durable. I enjoy this change as it adds more depth to the tactical layer and more than just a spray and pray of laser rifle and later heavy plasma shots.
The issue with this is that instead of balancing things around having heavily armored units like cyberdiscs and sectopods while also having units like snakemen chrysallids and mutons with say, beefy hp pools but low armor, it is instead the case that all alien units stronger than a floater or sectoid enjoy significant armor pools.
In order to combat these armor pools, one must utilize concentrations of firepower. Dealing the maximum amount of damage in one shot to have the armor "apply" the least amount of times. As if you shoot something 3 times and hit, the armor got to reduce the damage multiple times. And currently the only way to shred it is AP ammo and I think incendiary.
This fact coupled with the fact that ufo-extender accuracy for automatic weapons is painful beyond the first few tiles leads to one conclusion. Semi automatic weapons are superior in all cases. Including close combat, the 48-50 ish damage of a pulse laser rifle compared to its semi auto counterpart is pathetically weak when snakemen and mutons have 20-35 armor. Meanwhile the dreaded superhuman sectopod armor is nay uncrackable by anything but a heavy laser (heavy auto laser will not damage it on a maxroll of 200%) or one is to use extreme and dangerous explosive weapons. I enjoy the risk of either trying to chip away at the pod with heavy lasers or blast it out with 1-2 well placed fusion rockets/or an alien HE. (pro tip, do not give this to soldiers who are not psionically gifted and have less than 80 psi strength, or the ethereal will target their meager 60 psi strength and have them squadwipe you on cydonia.)
To fix this issue, I believe a more dramatic overhaul would be needed. By making 1 tile (non 2 by 2/tank/terror) aliens have increased HP but reduced armor, this could make automatic weapons a more genuine alternative in closer combat. With semi autos still king of aimed and mid range snap shots. While keeping the tank units with their heavy armor to make semi autos still useful against them with the heavy "tank buster" semi auto weapon class.
Lastly, it would be interesting if the arc shot of the auto-cannon was applied to all heavy semi automatic weapons. Giving them more of a role as they are currently even weaker than the auto rifles due to their TU cost. Perhaps making them arcing shots with small explosive radii (although this may change their damage type and mess up their balance) and then calling them say "laser mortar" and "terran plasma mortar".
Of course, these are just my ideas from the time I've spent in this mod. And I understand if you haven't the time. I currently believe it to be the best available as it injects a much needed difficulty spike while sticking true to the original. FMP X-FILES and X-PIRATES seem to be too easy, add too much, and eventually develop the issue of "super soldier" syndrome from the new games. The worst offense is that psionics are still insane, where as in this version the power fantasy of "bouncing heads" with a mind control chain to win cydonia turn one is thankfully removed. Not to bash the creators or fans of these mods, it is just a game after all.
Thanks and have a good day.