As Vanden noted in the comments, WOTC has "orders", and one of the orders boosts weapon upgrades. It boosts percent based upgrades by 5%, and integer based upgrades by 1.

so, while normally using "0" in the mod's config as the value for the prototype auto-loader indeed sets it to unlimited, what happens when you have the "boost weapon upgrades" order enabled is that it changes this value to 1 instead.

to fix this, whoever is using this mod needs to go to "C:\Users\(you)\Documents\My Games\XCOM2 War of the Chosen\XComGame\Config"

and find the file there called: "XComWeaponUpgradesExpandedWotC.ini"

open that with a text editor and change the value for: "FREE_RELOADS_PRT=0" to something other than 0. superior autoloader adds 3 for comparison. I changed mine to "99", since I cannot recall ever playing a map where I needed more than 100 free reloads.

Carry on.