You have maximum density for version 0, but when versions get sufficiently high then the numbers of functions there are sequences of bits with no valid interpretation because they represent primes or multiples of primes > the number of functions. Also increasing the versions of functions represented by larger prime numbers requires more bits than increasing the versions of functions represented by smaller numbers.

I think I would just represent the version of each function with a byte.

D'oh! Yes, any possible library contains only a finite number of functions to version. Even if we order the functions in decreasing order of update frequency, this scheme will overflow quickly if more than one or two functions update regularly.