I'm not an expert on Yoga by any means, but in all the classes I've taken (and with the exception of the "relaxation" poses), the instructors have emphasized maintaining a straight back. Spinal flexion hasn't been explicitly encouraged, unless (perhaps) it was in the context of a forward fold, where the goal is to relax the muscles of the back after some other strenuous exercise.
Also, reading through your links, the McGill fellow seems to have a fairly nuanced position on core strength. It's not as simple as "don't bend the spine forward".
Those poses show spinal extension, not flexion. It may be the GP was using the wrong word here. I've never seen a yoga class that focused on spinal flexion, but there are a lot of poses that extend the spine, and if done wrong they can cause injury. Most yoga teachers know this, though, and encourage students not to over-extend, either by keeping abdominals active as you describe, or by focusing the extension on the mid- and upper-back rather than the lumbar.
On an only slightly related note, why doesn't gecko spell checker recognize flexion?
I'm also not an expert, but in the classes I've taken (gentle yoga and basic yoga), the instructors almost always guide us in poses that involve "spinal rotation."
Also, reading through your links, the McGill fellow seems to have a fairly nuanced position on core strength. It's not as simple as "don't bend the spine forward".