Hi JohninCR,
From my experience, it is essential to perform measurements from the listening position.
I use an "Imp" by Liberty Instruments, and it reveals that minor rotations of a flat baffle affect the frequency response, both in cut off freq and in smoothness of response.
I now make my bass baffle adjustable around a vertical line compared to my FR, mid-range, baffle, and optimise the reponse for each.
Typically they both need to be at 90 degrees to the line to the speaker, but as you say, room effects mean that the bass baffle may need some subtle tuning.
David