Update: 2.5.32 is live now.
In the end I decided that companions stay normal quality. Quality makes a companion's equipment grid bigger, and that breaks the balance of every drone. A bigger grid also fits many more weapons firing at once, which can cost a lot of performance with a full fleet. I do have a fairly strict "do not police the player" policy, but here I had to make a call for the greater good. So a companion placed in a higher quality is now built as a normal one, on purpose. Sadly, the quality your companions already lost can't be given back. Please do read the README ('Information' tab) regarding the 'Quality' section.
The good news: equipment is the other way round. It now really gets stronger with quality. Weapons deal more damage per hit, roboports reach further, Flora's carapace, player support and Prism's healing all scale too, and shields and reactors work as in the base game. The tooltips show the numbers for each quality.
This was much harder than I expected. Sorry for the delay.
Thanks again for the report <3