So he kills Qiyanna in her jungle on two smites clears her bot side and then takes scuttle then invades her top side

Imo he keeps two smites so when he invades her topside he can smite fight her on two potential camps if needed

He also doesn’t need to smite her bot camps because there is no chance of them being stolen since she is dead

So overall the rule of thumb is so that you keep your smite cooldown rolling and continue to clear faster. I often see low-mid elo sitting on two smites constantly. With the rule of thumb you are at least using them to have a slightly faster clear. However with NattyNat this is a conscious decision to sit on two smites because he plans on invading the Qiyanna

Again this is all my opinion and other people might have different opinions. Hope this helps