While it's true you can flatten out the low first shot by setting the velocity at the bleeding edge of what the reg pressure can provide, the explanation doesn't make sense. Also the issues aren't when coming off the reg, they're occurring while on it.
So factory mode works with chrony feedback and presumably some form of gcu compensation for any reg pressure shifts to keep velocity stable. Much like an MVT airwolf did years ago, but with an easier job on the pressure side thanks to the reg. Yet the airwolf can keep the first shot velocity perfect every time regardless of bottle pressure, whereas the delta wolf can lose 80+ fps if you accidentally let it go to sleep for a split second. Somehow the airwolf also kept better ES.
Advanced mode either just loses the chrony and still maintains some GCU pressure compensation exactly like the Red Wolf (if you listen to several sources on AGN) or as you seem to imply above, just uses the exact dwell time you input like normal hammer spring tension (talk about going backwards?). Yet somehow it too will have a major drop in first shot velocity if you let it go to sleep for an instant without the reg pressure tuned as you described. All the while a similarly chrony-less red wolf or pulsar would be bang on after going into standby.
The reg pressure or any other physical characteristic within the gun, however set, cannot have changed significantly enough (if at all) in that split second to provide any reasonable explanation for the gun to have such a profound velocity drop after waking.
That leaves poor programming as the only real potential culprit, whether that be in the failure to write all the pertinent variables into memory at the time of going into standby, failure to accurately charge the board's capacitors on startup prior to that first shot, or some other bug.
The issue with tuning as described above is that you are currently severely hampered in your tuning options as you are basically forced to use a single reg pressure for any given velocity in advanced mode, with no wiggle room to eke out more performance or efficiency, completely negating the point of a gcu and it's fine control of the hammer strike. And factory mode isn't really versatile, its just useless.