I must admit I have never seen board and batten done below a chair rail. Is it possible you mean beadboard?
I think you will find there are many people who have done a two-tone paint treatment like that. But perhaps if there are going to be many imperfections in the wall, the better thing would be to paint the whole wall the same color, rather than draw more attention to it, and just paint your chair rail in your trim color for now.
Beadboard is not necessarily a gloss finish, by the way, so don't be concerned about that.
Good luck with everything. It is never as simple as we anticipate, is it?
Q