How about the idea of setting up each Quality Check to review the qualifications for a given model. Maybe even make it so that’s where you set the options for that specific model.
So, in gameplay, you could enter a dialog through the Quality Check station that would allow you to check off the items that you want to have present on the “approved” model that comes out. Add a “Reject” output to the station and a new slot station that would allow corrections to be made (although, make it more expensive to achieve a passing result this way).
That would make model/variant management much more easy to visualize (keeping track of models/options/variants now is a bit of a nightmare).
Of course, this means that the Quality Check slot would then become specialized in a specific model… meaning conveyor management would become a much bigger deal…