Adding this after additional playtime, it seems the discount from Mercantile takes effect after you finish the first Epione Lab quest and it increases as you finish more Protectorate quests.
After 1000H of playtime, this is the first time I notice something like this. I've checked it on static value items, like the Rocket Launcher BP, which I've found out is 9775 value, and White Phosphor Rockets, their value was dropping after each mission.
The wiki says nothing about this, but if this is intentional and not a bug, I kinda like it.
