I had just posted this on Reddit asking about this as well. Specifics:
with the directive off (for rifle):
280 Ammo - Maximum value
280 Ammo - What a crate fills you back up to
280 Ammo - What going to a safehouse fills you back up to
with the directive on (again, for rifle):
126 ammo - maximum value
126 ammo - what a supply crate fills you back up to
70 ammo - What your ammo is set to if you fast travel to a safehouse, even if you have more ammo.
(these values are what are in my reserves - not counting the ammo in the gun itself):
Yes this is a stupid problem to have and needs to be addressed ASAP.Ammo doesnt refill at safe houses or settlement.Even when I spawn there and had more ammo it will take it away.Only works when walk out then walk back into the settlement but doesnt work at safe house.
https://youtu.be/Ob2clmOLzxo