Muscle does affect our flexibility or range of motion. This is dependent on the number and ability for sarcomeres to lengthen, more specifically the titin filaments located at the end of the fibers. Within those fibers, actin and myosin do not stretch as they maintain rigidity to help produce force. When immobilized, sarcomeres are added at the end of the muscle during lengthened position, and reduced in numbers when shortened.
When relaxed, the muscles would be able to reach maximal length as neurotic signals of tension are not being transmitted; passive tension is the amount of force necessary to lengthen a relaxed muscle. Do note, that the connective fascia is the largest contributor to lengthening resistance in relaxed muscles and imposes greater resistance when muscular irritation occurs and is deformed (myofascial deformation). When external forces are applied, it allows the fiber to elongate (examples of forces can include antagonist muscle contraction, momentum forces, partner stretching, and even gravity).
In summation, if you got Muscle, let stretch them when we can.