I've just tried disabling plenty of mods and found out that you're right on point - Craft from Containers is causing this issue. But what's strange is that is still causes this massive lag-spike when picking up items even without almost any others mods - and somehow more people aren't reporting this issue? I'll try to fix it with some config changes or installing a different mod that does the very same thing, and will let you guys know if I manage to fix it