This is just like CLJ-1949, but for stubs instead of higher-order-function arguments.
The solution is more difficult, though, since {{cst/check}} and {{cst/instrument}} can be called/used seperately.
My only idea is to have a dynamic var where the two can coordinate. Stubs would use {{gen/generate}} when not called during testing, but in the context of a call to {{cst/check}} the dynamic var would contain an alternate implementation that works similarly to the patch in CLJ-1949.
I'd be happy to prepare a patch with that implementation (or any other) if desired.