digitalPulse() jitter/offset

Does espruino run another one on top of it?

Yes, but for something like digitalPulse there's one job queued up, so there is no real overhead involved.

Espruino's timer implementation could be improved (eg. for digitalPulse there's no need to use the current time at all), but it's reasonably low priority at the moment as it's quite a big change and it works fine on official boards. There's an issue for it here: https://github.com/espruino/Espruino/iss­ues/1444

If you really want accurate timing without actually buying an official board it's possible there's some spare timer hardware on ESP32 that you could set up yourself with peek and poke.