.. don't think I would be too concerned about high flap drag on TOR acceleration .. measurable, but probably not of concern other than for the case of critical runway length with no obstacles and for the one flap setting .. far more important consideration is the speed schedule differences between flap settings which will swamp any minor acceleration delta.
The other consideration is WAT limit .. higher flap normally has a lower WAT limit.
A case of balancing the runway limits against WAT and obstacle limits ... circus juggler is a good CV point to look for when employing ops engineers.