I'll try to express myself better if my answer was inadequate: no, they are not generated on the fly by design.
Right now, stencil scripts are stored in the content store, and there is a link to the store using the store_id (see my comment above).
The stencil script is created when the stencil is saved. If there are existing scripts, they are merged and the merged result is stored again in the content store. When they are needed, they are fetched from the db and content store (and cached).
In theory, you could remove that, and on bootup walk through all your stencils, parse them and execute similar logic and put them in the cache. But that's theoretically and as far as I know, nobody has tried this path yet.