I think the "Guard" you meet in-mission are likely to end up being PDF troops, and thus would be more likely to carry their world's production autoguns (as a lore excuse for why yours are shooting autogun rounds, I haven't seen that yet in rescue sub-missions but it's certainly odd) as opposed to Munitorium-mandated lasgun patterns (easier to supply a less standardized munition on the homeworld/in the home system).

Just helping maintain your suspension of disbelief so you can more righteously smite the heretic, purge the mutant, and burn the xenos!