Afl-fuzz runs a program until main() and then forks it repeatedly. An empty main() can be called at least 10000 times per second this way.
With AFL++ you can even determine exactly where the fork happens:
https://github.com/AFLplusplus/AFLplusplus/blob/stable/instr...
There needs to be a way to dynamically link a binary into your own address space, and call it's logic repeatedly, without incurring all the process startup overhead all the time.
Pretty much, have all command line utilities be linkable like a library.