When completing activities in the open world, any activity that rewards an equipment item will reward one of the type of targeted loot for the area unless the targeted loot is Skill Attachments. The rewarded items is always something other than a Skill Attachment.
Gear System Mods are rewarded correctly.
I've only noticed this since switching to a PlayStation 5 but assume it's not specific to that console. I do not have my PlayStation 4 setup anymore to go back and test but this fairly easy to replicate.