The Physical Projectile Damage tech increases the damage of Bullet magazines, Shotgun shells, Vanilla Gun Turrets, and Scattergun Turrets. However, it does not increase the damage bonus of Heavy MG Turrets (or Gatling Turrets). As a result, at PPD level 6 and above, vanilla gun turrets start to do more damage per bullet than Heavy MG (& Gatling) Turrets, which feels out of line given these heavier turrets' base increased damage.

(On an unrelated note, I'm amused by your icon choice for Scattergun Turrets. They do look a bit like 1400s don't they?)

It's intended. I had those bonuses as a separate research in versions 3.X.X. But that made all ammo turrets OP as hell. So that has been taken out.

HMG's might lose the DPS advantage to Gun Turrets at yellow science, but you still get the range and sturdiness benefits - range specifically is worth still having them.

I suppose that's fair. Feels a bit inconsistent but then by the time you get to yellow science you have a bunch of other defense options to work with, so it's okay to have the HMG be an early-game powerhouse that falls off later.