I share your experiences and your head scratching. But I ask again, at what point is open stupidity addressed and challenged ?
The National Explosives Management Authority (I might have missed an "A" for ammo in there, still on first coffee... ) has much more control over ammunition management on the ship than some might realize. And of course, the Ammo Tech Authority does as well, who certify our magazines and ammunition safety standards. Neither of these organizations is RCN controlled.
There is also a new NATO rule where a ship that carries ammunition that isn't a warship can not go into port unless it's to load or unload that ammo. This means if JSS is classified as a non-warship could not go alongside Halifax unless it unloaded all its ammo every single time!
And the last reason is that an ammo accident on a warship is far far worse than one in a LAV. Not only in potential lives lost but in strategic impact to Canadian security. Historically the Halifax disaster likely adds some trepidation.
Despite all this, there is definitively some pushback. Ship internal ammo transfer rules were imaginary, and Sea Training 2 years ago clarified them. They are far more permissive than they used to be. 1. Clear the route. 2. No smoking or cell phones within 2m of the route. 3. Use two hands for each "unit" of ammo. That's basically it.