Yep. It gets at, what is the meaning of "faster?" Implicitly we are saying the average runtime of A is smaller than the average of B.
But if for example, B always halts in 10 seconds, and A halts in 1 second 99.99% of the time but A runs for 10 years 0.01% of the time, then A is "slower" but you'd need 10,000 trials to notice.
But if for example, B always halts in 10 seconds, and A halts in 1 second 99.99% of the time but A runs for 10 years 0.01% of the time, then A is "slower" but you'd need 10,000 trials to notice.