OK here you go, this is the SDL release on the screenshot archive:
VisualBoyAdvance.cfg
You are looking for a line:
# Video setting. 0=1x, 1=2x, 2=3x, 3=4x.
video=0
Anything but 0 will rotate the screen 90 degrees.
Hopefully this will save someone some time in the future. Thanks for those who helped me track this down!