greenimi,
Theoretically the constraint provided by datum feature B of the translational DOF along the axis of datum feature A shouldn't have an impact, however in reality it depends on what exactly datum feature A is meant to be as currently it is (as noted) applied incorrectly to the axis as well as what the assembly condition is. If it is meant to be the stubby diameter (40 -.025/-.064) to the right of the flange face (datum feature B) I think you'll find that the reality of the high diameter to length ratio will cause some issues during measurement if only datum feature A is utilized.
Furthermore it is highly likely that the assembly condition would dictate that the flat flange face datum feature B should be primary - if you note in Y14.5-2009 pretty much all of the examples utilizing a flat face as a datum feature have it as primary for this reason. Take a look at fig 9-7 for what seems to be a similar case with a flat mating face and what looks to be bolt holes.