His not saying his Yoga/Pilates/Stretching is universally bad. He is staying that some of the things that yoga and pilates recommend can actually make your problems worse.
Take, for example, the forward fold which I've seen recommend in a lot of places for desk workers that experience lower back pain. So you sit all day at your desk with your lumbar spine (lowest part of the spine) in flexion all day. After some years your back back starts to get a bit achy. Maybe a little disc bulge because your vertebrates are asymmetrically pressing on your disks for 10 hours a day. Doing a forward fold will only further aggregate any issues you might have. Because you have already spent 10 hours a day for years with your back in flexion. Flexion is your problem, not the solution. It is like have a sore thumb and then start hitting it with a hammer to try and fix it.
If you have backpain from sitting too much. Blindly starting to bend and twist your lumbar spine is not going to solve anything. In the worst case it will only make things worse. Instead do lots of core work with neutral spine and work on some hip mobility and try to rediscover those glutes you forgot you had.