The master switch, if turned off, will override all section switches and autoswath(check marked in box, on).  If you turn off section switch 10 it will override autoswath(check marked in box, on) and not allow the clutches to engage on that section while the other ones continue to plant. 

With autoswath on you could shut off individual sections via the appropriate section switch or turn everything off via the master switch.  There is a setting under autoswath section control that you can select for the outside boundary options either "Keep Swath Section Unchanged" or "Turn Section Off."  If your worried about sections the outside section flickering on/off you could change to "Keep Swath Section Unchanged" and run with autoswath on as it would ignore turning the outside section off if it got beyond the outside boundary.

All we do is shut autoswath off on the first pass around the field and then turn it on after that with no problems.  The reason we do this is some of the boundaries aren't the greatest and the first round we are always jockeying the planter around so it seem logical to run autoswath the second round when the going is smooth, that's my .02.

Stopping momentarily to engage/disengage autoswath doesn't take the productivity out of the day and we have ran seed command for 3 years now and feel it is a great product that is reliable.  It may not be an easy feat for the engineers to change some of the programing to add in specific details that you are inquiring about.  The best thing to do is let the AGL sales rep and support know you are interested in adding a feature like this an hope they will consider it for future releases. 

I tried to think through as to why you want to be able to have a feature that allows autoswath to be selected for particular sections and other able to run manually but I don't see a case where this would be useful to me.  Seems like it would be too confusing to have some sections automatically running and others manually running.  It makes a little more sense in spraying than it does in planting. To return to automatic control on the Boom Pilot do you turn the section switch back off then?