Tried to get into Transport on the IE dev server, but i cannot add a quarks chests.
And on the server the vanilla ones are uncraftable.

Using forge:chests instead of the vanilla chest item directly i think should be a good idea

Would be a horrible idea, actually! As all Module's are meant to be one to one with their blocks. A better idea would be to revive the old Quark Compat that had Cargo Modules for all the Quark chests.