An Excellent point. So, let me make another point to help with that.
While training, Whether it be vaults, precisions, or landing, try not to Bend your knees past 90*
Jumping and Precisions you will have to exert more pressure on your knees then necessary to bring your body upright. It is counter productive
Remedy Instead of over bending your knees, trying swinging your arms more. Swing them back when your bending down, and forward when jumping. You should notice a considerable difference.
Vaults This is an uncommon problem, but I have seen it before. Again, too much force on knees, also your approach will be low while actually vaulting, which could result in you tagging your foot or something.
Remedy Try pushing and lifting your body more with your hands when they are on the rail/obstacle. A little upper body conditioning goes a long way.
Landing This one is common. Also the worst you can do. Although landing a little past 90* is okay here, but when you land with alot of weight on your feet, it put a huge amount of pressure on your ankles and knees. Its is very bad for you.
Remedy While landing, lean forwards and put your hands out. This will relieve alot of the stress and pressure from your lower body joints.
Parkour is a full body sport, and relying on just your legs is more harmful then good for you. Also, for the actual degree that you shouold be working at, it varies from person to person, but 90* is a good average.