I use controller and use both sort and custom. I use sort when I have all the items in my inventory I want to keep and let the rest of the inventory slots be filled up as I play through out the day. Then I sort what I got manually...in reverse. I put all the stuff I want to hand in for GC seals at the very bottom and the stuff I want to sell to npc right after it while keeping the stuff I want to throw to my retainer right after all the sorted inventory from before. Then I keep playing again until I stop by a city. I have never accidentally auto sorted my inventory.

Prompts for this are absolutely unnecessary.