There is no problem with stretching the muscles, in fact it's the short muscle that will be strained when something happens that stretches it beyond it's normal point. They say a lot of body builders are musclebound and this is usually because they don't work their muscles in the full range of motion, so the muscle shortens. When it gets to a stretched extreme, then the muscle isn't used to being in that stretched position and that is where you get the strain. An example is what your book said about flexing your feet instead of pointing them. In this position, you are stretching the back of your lower leg, so when you get into a sprint the muscles are used to going from pointing to flexing.

For cycling, you are using your hip flexors and hams as well as your quads, so an all around program of strengthening and stretching is very good. Most folks have tight and weak hams, so it's good to work on them too. All exercise should work the muscles you use and the ones you don't. An example would be a basketball player. They spend a lot of time pushing the ball forward, so their pecs become strong and tight. Because of this, their upper back becomes stretched and weak, so they end up having chest and back problems because they are unbalanced. They need strong pec's to do their job, but it's really important to stretch the chest muscles so they are not tight and less likely to strain, and to tighten up the upper back so they don't have a weakness.

In any activity you want to make sure you do a well rounded exercise program. Like for cycling, it's recommended to have strong core muscles, so stomach, low back, sides. Nothing too weak and nothing too tight. That is what helps you to be your best and hopefully avoid injuries.