While he may not get the full dose benefit, depending on his transit time, the XR formulation is more of a continuous release, as opposed to the burst of medication you get with the standard formula. This gives you a more steady blood level, instead of the peaks and valleys of the standard Effexor dosing.
So, even if there might be some waste, it might be a better option and better over-all result. That said, the proof is in the pudding. If he exhibits symptoms of withdrawal or under dosing, he will need to return to the split dosing with different formulas, increase the daily dose, or take smaller doses of the XR, but twice a day.
Good questions to discuss with his doctor. Each patient needs to be treated individually. Even discounting the shorter length of gut, he may metabolize the drug differently. Hope this helps give you some perspective. I am sure you already know it is never as simple as it seems it should be!
Jan