Ultimately exceptions are a question of balance. The seed vault is blocked because it would completely redefine the farming and herblore meta removing the game mode defining "keep/drop" decision for seeds entirely. Other exceptions like our death mechanics and POH storage are more about sticking mostly to the original mechanics when those systems got updated for mains. But what would, even completely, removing the UIM cargo hold nerf allow us to do that we can't already do in better/more convenient ways?
Cannonballs: we can already carry as many as we want in the bag and we generally want 0 as a Dwarf multicannon is basically never used and its not because we can't carry enough cannon balls.
Fish: It would be limited fish compared to the unlimited fish we can store in the form of minnows and tempoross loot. They would also be in an inconvenient spot compared to banknotes in your inventory. I'm really struggling to see me going out of my way to keep that stocked up on a pvm grind when the humble cheesy potato is right there and brews are baggable and unnoting at any bank vs running back and forth from my boat seems way more convenient. And you wouldn't have to take resupply breaks nearly as often as even with a completely uncapped hold its still limited fish compared to our other unlimited options.
Are we even going to be able to do future late game sailing content if we are so limited on boat food? If there is ship combat in raids 4 is it going to be balanced around the few of us UIM's that can only carry 9 boat food when the vast majority of the player base will have over 10x that? It would either be a cake walk for mains or impossible for UIMs. Imagine having to do every PVM encounter with just 2 inventory slots worth of supplies.
I do think the devs made the right launch decision. Better to start off safe and then buff later then not worry about it at all and risk breaking the game mode and having to nerf. And its not like they could of polled it or anything because without getting our hands on the skill we couldn't really make an informed decision.