The thing is, I actually tried this. what you're saying, I do not see it.
I built the companion drone, and some of the companion equipment, and put the companion equipment in the companion drone, with no issues.
Then again, I tested with all of my mods, plus the Companion drones mod, and nothing else. If you have something else installed, I would need to know that information, but it is likely that if you do have other mods installed, then those mods are breaking companion drones, not mine.
You'd be surprised at just how many mods try and integrate into, or change my mods, and break other mods in the progress, it is not uncommon, in fact it's very common. I get more bug reports for issues about other mods breaking each other when mine are installed than I do about bugs in my own mods.