When using the Quality Effects mod, (adds module slots at higher quality) added recipes become missing in any quality machines. Only normal quality machines have the new recipes. Are the new recipes hard coded to only the vanilla machines? More likely an issue with the Quality Effects mod as it's implementation is a bit janky, but I thought I'd ask anyways.

The mod in question: https://mods.factorio.com/mod/QualityEffects?from=search

Honestly i have no idea
I think you should ask the maker of the other mod because i do not know how that mod is coded and i do not know how to fix that cause of that