There are options to make quality scale the number of module slots a machine gets - if you have a ghost with those bonus slots, this mod only puts as many modules into it as it would have at common quality. I need to open the remote view and ctrl+click the ghost again with the module to get all the slots filled.

Quality Effects is one such mod that adds those slots, and you can also do it with Adjustable Quality and changing the startup settings (which is what I am using currently).

looks like that mod predates crafting_machine_module_slots_bonus = true and has not been updated since.

i would suggest looking for another mod that does the same, i am currently looking around to see if there is one, and otherwise i will be making one.