I hear much talk about restricted or supposed 'safe practises' with movements when weight bearing. "Squat only to parallel" and "Lunge only to 90 degrees flexion" are examples of cautious attitudes in regards to training and technical instruction. Too often I see issues in clients (primarily knees/hips/lower back) that have been brought about by strain and wear on tendons/muscles where half range of motion has resulted in excessive weight bearing in compromised positions, not allowing muscles and joints to work within a full Range of Motion (ROM).
A muscle, to maintain health and function, should work throughout its full capacity to ensure that tendons and muscle fascicles (bundle of muscle fibres) are utilised to their full length and capability. Much like a rubber band, if you don't use a muscle at its full length, it will shorten and not be used to operating when it is asked to extend fully. Hence it will strain and possibly break when placed under this pressure. "But when i go to full depth or extension, it hurts and I can't lift as much". True - it is much harder to maintain alignment and form at the end of your ROM because that is where you require the most stability. Doing a full squat to the floor is harder because your muscles have to work at their full extension. So you cannot lift as easily or as much, however you are forcing your muscles to operate at their full capacity. Training to this depth or length of extension with safe technique should encourage more strength and stability of a muscle or joint as it adapts to the load placed upon it.
Shortening muscles from not working at a full ROM, leads to hypertrophy of the muscle and thickening of the tendons without allowing the 'normal' ROM of a joint. An elbow is able to extend (in normal function) to 180 degrees (nominally). Excessive shortening of the bicep tendon will result in a tendon that will not allow this full extension. If the joint is forced into full extension by an external force or action (eg. an arm bar in Jiu Jitsu or weighted bicep curl even a forehand in tennis) does it not stand to reason that the tendons which are 'uncharacteristically' short will tear under the unaccustomed ROM?
Outside the weight room, on a field or court, when going for that deep ball in a volleyball pass or bending down to jump over that bar, you need full depth and stability at that particular point to make sure you don't collapse on the floor under induced pressure. When the adrenalin is pumping, you need to know you can perform extra actions without worrying that the increased ROM is going to tear your muscles apart. This is functional training which should be a consideration in any training regime. ie being able to perform the movements you need with assurity and stabilty.
Full plie's in ballet and full squat cleans in weight-lifting are 'arse to the floor' movements. Once going past 90 degrees flexion, the load on the patella is 7 x the normal strain. That's a lot of pressure. Any deviation in technique or 'alignment' of the patella at this point is dangerous. Mis-tracking and poor alignment can only result in pain. However, dancers and weightlifters do MILLIONS of plies/squats over their careers and can still find themselves healthy and functioning long after their performing days are over. The oft quoted "bad knees from lifting/dancing" I believe is more a result of bad form and technique rather than the action itself. Form and alignment in technique is paramount to ensuring effective function. 'Training' this technique comes about by repetition. "You become good at what you do regularly". This ensures full ROM is not only achieved, but safely trained in order to perform what may be perceived as irregular or excessive movements with confidence.
In almost all athletic movements, 'elastic recoil' precedes concentric contraction. This is where the muscles perform a short lengthening that recruits stored energy to help perform a powerful consequent concentric contraction. Stopping halfway in a movement places the muscle under isometric contraction. In this state, by asking it to contract again to return to the original position, asks muscle fibres to concentrically contract from an isometric position, thus avoiding any 'recoil' or recruitment of latent power in the action. Without this recoil, are you placing increased load on soft tissue fibres to not only stabilise, but also concentrically contract to effect movement?*
Compensation in movement patterns to effect a 'safe' training, is an individual requirement. Some people don't have the flexibility to press a bar behind their head or bend past 90 degrees flexion of the knee. Everyone has their own idiosyncratic bio-mechanics and what works for one doesn't necessarily work for all. However, I believe just as a yoga practice develops and expands according to your own ability and increased ROM, you should always be aiming to find further ways to advance your stability, power and strength, even with 'excessive' flexion/extension. Stability in these motions, requires repetitive reinforcement of the muscle in that position. To effect safe movement patterns, working to increase ROM to full extension with correct alignment, should be promoted to effect stability and 'safe' practice.
Reducing the ROM reduces your ability to handle gross movement actions. Whether that be kicking a ball, lifting a weight, or jumping over a hurdle, knowing you have the 'trained' ability to handle that ROM with strength and stability is a healthy state of physiology and will help avoid injury.
*Supporting evidence can be found in studies from Tokyo (T. Fukunaga Dept of Life Science [Sports Sciences] - Univ of Tokyo) which states: "more compliant subjects would benefit from enhanced tendon recoil and more advantageous force-velocity and length-tension properties of the working muscles".