I was looking through my damage bonuses, and noticed that while the scattergun and vanilla turret get a damage bonus from physical projectile damage researches, the other various turrets from this mod are untouched. This seems to lead to the base game gun turret outscaling the modded turrets in damage as more research is completed. Was this an intentional design decision? If not, could the various physical damage turrets from this mod get that bonus as well?

(The beam turret, pulse laser, and thermal laser turrets seem to be getting research bonuses just fine, so I'd thought I'd clarify whether the physical damage was a deliberate outlier or not.)

Deliberate. Stacking 2 multiplicative damage bonuses (from ammo and the turret) gives way too much damage, ESPECIALLY now that quality ammo gives yet another damage increase. Gun Turret and Heavy Scattergun have it, because their range makes them basically trade blows with Spitters no matter how much +damage you have. But yes, Gun Turret eventually will out-DPS modular HMGs and (much later) Gatlings, but that's fine - if you're into several infinite damage techs AND quality improved Gun Turrets for range, you've earned them being that strong.

As for modular Cruise Missile/Cannons - stacking damage modifiers made them AoE one-shot behemoths pre-infinite techs, which was way too much. You already get +100% damage per infinite damage tech for cannons. With uranium shells and early infinite damage techs, Heavy Cannons will do that anyway, especially with quality ammo. Cruise Missile turrets are support, they are not meant to clear whole attacks by themselves. One-shotting Big biters with Explosive rockets is enough, you can always use nukes for ammo after all if you REALLY want to full clear attacks.

Duly noted! I didn't realize that the damage was multiplicative, not additive. I appreciate the detailed response. It's a tad annoying, since the restricted angles for the modular turrets makes far more useful on space platforms for ammo efficiency, but I'll bodge something together that'll work.