Let's create an application that can take any of 10000001 model specifications (text file or some rudimentary form of user input), and create the model in Unity (despite and with full knowledge of warnings to do model-building in other 3D apps).
Would it be better to do this at runtime (the models could be simply a set of 3D coordinates and we can use prefabs)?
Or, should we pre-compute all the potential models and store them as some kind of call-able library?
This is one of those situations where it really depends on what your goals are.
If your question is "is loading time going to be too long if we have to generate model data", then that really depends on the amount of data you're processing and the speed of your target machines. Assuming you already have the tech set up to build your models from data, just benchmark it and see if loading pre made models is worth it.
You might be able to write an editor script to save out a model made in Unity. I'm not sure how that would work, though.
Edit: What kind of model building are we talking about here anyway. Are you talking like making actual models from point data, or just piecemailing pre-built pieces? Sort of like making a model of some furniture using things like "use leg X at transform Y"?
If it were me, I'd look into a more flexible solution like an obj importer:
But of course, it depends on your needs