Ah, sorry, I had misread you to mean "if you try to use the B you've already got (from tuning for G major) against a drone in tune with the E you've already got (from the A) it won't work. Because, as you explain, the B would need to be sharper. It is strange, I find, that Mike Nelson explains his lower tuning for the bottom E as being for the sake of G major rather than for permitting E minor. I have my low E a bit flat relative to the top E and this permits me to play in E minor quite successfully (it was tuned this way by the maker).
The middle E even tho it is tuned as a perfect fifth against the A drone does not sound too sharp against the G and D drones strangely enough. The interval C-E can sound a bit odd tho, at least to my lugs. chirs -- To get on or off this list see list information at http://www.cs.dartmouth.edu/~wbc/lute-admin/index.html