It's certainly a good idea to have some built in method to prevent stone build up.
That being said, you can manage stone build up decently well if you know what you're doing.
Just a question - if you build constructions out of the stone, its less painful to the CPU/Memory then if you have a ton of rocks lying around? Or not?
I'm pretty sure that any object including blocks or constructions make the memory hate itself. Things used in constructions are still tracked but I don't know if it's the same or not.
To be fair, lots of stuff doesn't seem to slow down your game that much, it's just a critical limit after which you'll continually crash.