No, the pulses are synced in hardware. Should be the same clock driving things. It’s not like the pulses are synced to whenever your software runs. Even if that were a potential problem, you’d still be alternating the load, and thus distributing where the heat is being dumped.
For that second bit, I’m mistaken. You’re right that if they were not synced it’d be an issue, as it would potentially be as if there were no PWM or a higher duty cycle, rather than the LEDs being completely cut off, so it wouldn’t be distributed like how I claimed. But yeah, in light of things being hardware synced you don’t need to worry.