I have no problem at all with you making brushes from any map I do. Go for it.
As to the problem with the overlap, I don't really think there is a solution to it if you use the brushes in a normal way. The brushes aren't two-tone but go from black to transparent.
I did read in another thread recently (sorry, can't remember the poster or the thread) of a way to place a brush and then use clone to make it work in a way in which you desire but when I tried it I couldn't really get it to work.
Again, no problem at all with you making the brushes. Good luck and I hope they turn out good.
Edit: Oh, and one way you might consider to work around your problem is to use more than one layer when placing your mountains. When I did Vaniya I used four or five layers and if a mountain was placed across another then I would make sure it was on a different layer, that way it was much easier to just delete the part of the mountain that was hidden. Hope this helps.