Well, if we look in very basic detail at how muscle contraction works within a myofibril of the sarcomere:
N.b. this isn't on a loop and only plays through seven times
The red lines represent actin filaments whilst the blue lines represent myosin filaments. During muscle contraction the filaments move over each other:
As shown in the above diagrams the "more contracted" a muscle is then the smaller the size of the H zone (the area where there are just myosin filaments).
So if we consider a penetrating impact that went through a plethora of identically aligned sarcomeres (obviously this is not the case in nature) then we could presume that (et ceteris paribus) the object would not penetrate as deeply into a contracted muscle as it will hit more tissue on its route than in a relaxed muscle.
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