This only occurs when mods depend on the epic-quality and legendary-quality technologies (known to you as Epic Quality and Legendary Quality) before my mod loads. This makes it somewhat inconsistent which mods are incompatible for this reason - and as such, I will keep this thread open for people to tell me which mods are incompatible - so I can notify the developers of those mods in a developer-friendly way which will tell them exactly how to fix the issue.
I will also move certain modifications of existing prototypes into the data-updates.lua file so that incompatibilities with some mods don't occur anymore.
Also, hooray! 2K downloads!