Hi Ashlea!
I think you’re right, multiple uses of -include is effectively an AND operation. You could do A OR B by combining the two regions into one single mask (e.g. using mrcalc) before feeding that to -include. You can do this in one step (sorta) using bash piping or command substitution like this:
# With a pipe
mrcalc A.mif B.mif -or -datatype bit - | tckedit tracks.tck -include - A_or_B.tck
# Or with substitution
tckedit tracks.tck -include $(mrcalc A.mif B.mif -or -datatype bit -) A_or_B.tck
I’m not enough of a bash poweruser to know the practical difference between those options though (something something, subprocesses and variables… 
) so I’d say take your pick.
Hope that helps!
Fiona