This appears to be working as intended... the Loader Storage Chests are specialized chests that the mod uses to return items when upgrading or picking up turrets/vehicles/etc. If there is not enough room in the Loader Chests, upgrading of ammo and auto player inventory cleaning of picked up ammo/fuel will simply pause until space becomes available. The Storage Chests from this mod are not meant to replace the vanilla logistic storage chests.
Let me know if you have any more questions!
Edit: To clarify, the logistic filter on my mod's storage chests only applies to items logistics bots may put into the chest, and not to items my mod puts into them script-side. I'll try to implement honoring the logistic filter in the next update though. I'll let you know if I get it!