The mod Alien Loot Economy(https://mods.factorio.com/mods/sensenmann/alien-module) implements modules that level up with the number of aliens you kill. But what I noticed is that the modules don't level up when inside factories. I do not know which side causes the incompatibility, Factorissimo or Alien Loot Econ.
What is most annoying is that I haven't found a way to level up the modules once they are stuck to a lower level. They do not stack anymore and occupy inventory space. I just recycle them with Black Market, but that's not really an intended method to get rid of the broken modules.