Megkerestem a választ, szóval egymásra rakódnak a perkek:

"Once a certain satchel has been unlocked, the perks that come with it become permanent, and thus stack across all satchels. For example; if the player unlocks the tonics satchel, but then switches back to Arthur's default satchel, they will still be able to carry more tonics in the default satchel than they would before unlocking the perk."