Sorry for the delay in answering, been busy with course delivery.
Generally, in overuse situations where you talk about eg bench press, it is the fascial sheath that shortens not muscle. Fascia is designed in a criss-cross fibre matrix, thus has the ability to adapt to the structure it contains. Muscle fibres are more longitudinal, thus contract or relax in the 'all or nothing' rule. So tightening in this situation will be myofascial sheath shortening.
My ideas on sport fitness is more along the lines of training in the manner the body is going to be used in the particular sport. For example, why should a swimmer spend time running, or pumping iron when they want their body to swim? Similar with a track athlete, why should they swim, or do squats, or as i have experienced, pull tractor tyres around the field, when they are meant to be a sprinter? I believe the training needs to fit the sport more than it does now. Even training in the gym to bulk up needs to be more dynamic and asymmetrical, trying to use the body in the manner it is going to be used in sport. Symmetrical movements are very rare in sport. When do you see a footballer doing a squat motion in a game, or a golfer doing a bench press motion in a game? Gym work does not fit the sports activity well enough, it focusses too much on muscle bulk and strength at the expense of flexibility and natural asymmetrical body activity. If I was a runner and ran marathons, I would run...nothing else. If i was a swimmer, I would swim. Why train the muscles in one way in the gym, and then expect them to function in another way in the sport?
Your point on not comprimising the joint stability, I think it would be very difficult to stretch to the point of causing irreversible laxity in the joint structures, ie ligaments, capsules etc. These structures are laden with sensory nerve supply, and the pain is there to prevent this from happening. Stretching maintains flexibility in the short term. Collagen has a life of between 300 and 500 days, and as fascia is mainly collagen, it can in the long term alter shape, so stretching can benefit long term, but don't expect radical changes in the short term.
Increasing muscle bulk will stretch fascial sheaths, but working the myofascial unit in a small range will allow the fascial sheath to adapt to this position, thus limiting the space for muscle growth.