Hi Amber ... good question. I often see super-flexies in my Yin Yoga classes. They don't feel much, but there are still benefits for them in these poses.
Firstly, they are keeping the range of motion they currently have. Over the years, even the flexies will get tighter as their joints shrink-wrap with age. Secondly, many of the poses are stimulating the meridian lines through the connective tissues even if the joints themselves don't feel much stress. To increase this stimulation, the student could engage the muscles, as you suggested. However engaging the muscles will not help the joints become more stimulated.
One suggestion Paul Grilly has made, jokingly, for these poor unfortunate students who are so cursed by being flexible that they don't feel anything (compared to us normally folks who get a wonderful sense of being pulled apart by the poses), was to dig a pit under the student so she could actually fold through the floor and get lower.
Well that may not be practical, perhaps, depending upon the pose, there are ways to use props to allow the student to create more space, allowing them to go further.
These are my current thoughts. I would be interested to hear how others address this topic.
Cheers
Bernie