"After an extended descent, I do get some discomfort in my knees."
That has nothing to do with your choice of footwear. Far more likely to be a muscle imbalance or just plain lack of training, presented as overuse.
Sure, that's true. But the OP asked how much it mattered if he actually bought stability shoes or neutral ones – at this point it doesn't necessarily matter WHY he has that imbalance, he is going to use those shoes NOW and he has to function with his muscle imbalance. Usually the knee pain with descending is because of weak hip muscles allowing the entire leg to roll inward…but guess what? It usually takes 6 weeks for the effects of training to show up. In the meantime he should own a pair of shoes that will help him NOW… Stability shoes will not matter in the least at this point in terms of limiting his ability to train the appropriate muscles. But it can mitigate the internal rotation of the entire lower kinetic chain, which will ease the aberrant forces through the knee.
I know you guys love barefoot and minimalist shoes, but seriously, there is no one size fits all prescription for foot performance out there. Shoes can be a tool both to train (minimalist), and to help to prevent injury or to protect joints and allow them to heal (not minimalist).
In my own case, for example, I have significant cartilage tears in both my hips, one of which has gone through 2 major surgeries to try to fix. I have a heck of a time maintaining strength in my hip muscles and consequently my R hip rolls all over the place…if I wear a slight motion control shoe I find I can walk all day without my hips acting up. If I walk in my vivobarefoots…which I love, by the way, for more than a few hours I literally can't move by the end of the day. In my case it's not my feet or ankles, which are strong as can be…but further up the chain.