it's good to hear you like pcb2gcode!
I use etch_z_adjust only with the gcode files for the front and back side, and never used the milldrill option personally.
If the probing grid is not too dense, it should be possible to drill the pilot holes first, then mill the back side, but that would mean having to probe the board a second time unnecessarily.
I too suspect you should be able to just insert the body of the drill file after the preamble or before the finale of the back file, then run etch_z_adjust.
It's not possible to have pcb2gcode do this automatically yet, but it seems to be very reasonable and should possibly even be done by default if --milldrill is used.
I'm going to be away for a week now, but I have a whole week in August just to work on pcb2gcode and will probably fix this.
If you have any further input I'd be interested to hear about it.