WHAT IF we keep the current cargo based cloak fuel system but we add a piece of equipment called the "fuel tank"?
The fuel tank would of course contain ammo based fuel, but since it is a dedicated fuel containment system it would provide 3x the fuel (for mk1), 2x the fuel (for mk2) and 1.2x the fuel (for mk2a). (the numbers of course need to be adjusted for balance, but the general idea is that dedicated fuel tanks offer higher fuel capacity than the cargo hold but takes up space in the cargo hold)
An mk1 tank could take up 40 cargo space and provides 120 cloak ammo capacity.
An mk2 tank would take up 100 cargo space and provides 200 cloak ammo capacity.
An mk3 tank would take up 400 cargo space to provide 480 the capacity.
You could further balance this out by making the fuel tank hardpoint visible and easy to destroy.
The benefit of this is of course forcing you to set aside dedicated cargo space for fuel tanks, while allowing people to still use the cargo space for carrying fuel (albeit less efficient in terms of cloak time)