I have some ideas e.g. I like the interim data uploads for animations to be in these notebooks. Why? Because then I could do it once and train my engineers to basically use my notebook and replicate the code while changing data.
For example, I will code the interim steps for the orbitals probability cloud animation we discussed, then other programmers just use the notebook for the new orbitals (there are 100s of them).
As it stands today there is no notebook concept for Clara or three.js .
For years we do this with Mathematica notebooks for our trainees and has worked nicely.