Well, of course, if you knew all that, and could enter it into the ELS, it could compensate, but the Clough42 ELS is not set up to do that math. Looking at the over-threading, my guess is that this is still an issue related to disengaging the half-nut and trying to re-engage it at the proper time and place. He's using the ELS that James Clough designed, and James goes into what's required to do metric threading with his ELS in glorious detail in the video at the following link. It's not straight forward given that he has an imperial lead screw and trying to cut metric, but it is possible to be successful disengaging and re-engaging the half nut if strict procedures are followed. Personally, I would find it a lot easier to just leave the half-nut engaged and back out of the operation for the next pass even with this ELS.
Let's ask the OP - were you disengaging and re-engaging the half-nut between passes?