Since modded squads are added by replacing vanilla squads, it is possible to earn a vanilla achievement with a modded squad. I am not sure if it is possible for us to prevent that, so this issue may remain open for a long time.
Perhaps ideally we could convince the game after starting that we are custom squad instead (tracking that the squad was properly selected for modded squad achievements). Not sure that is possible, just the best idea I have.
Since modded squads are added by replacing vanilla squads, it is possible to earn a vanilla achievement with a modded squad. I am not sure if it is possible for us to prevent that, so this issue may remain open for a long time.
Perhaps ideally we could convince the game after starting that we are custom squad instead (tracking that the squad was properly selected for modded squad achievements). Not sure that is possible, just the best idea I have.