No, you do not want to have the rubber shield in the cable stop. As you relate, it would effectively change the length of the outer cabling as it is compressed by increasing cable tension. This would adversely affect shifting performance.
As pictured, the rubber shield is positioned correctly. The cap with tongue should be pressed fully on the outer cable and then fully inserted into the frame cable stop. The tongue proceeds through the cable stop opening, surrounding the inner cable. A Feature near the end of the tongue is a little raised portion. Sort of a little square or rectangle that blips up from the tongue. This little feature helps to hold the rubber shield in place. In addition, the smaller opening in the rubber shield is still a little larger than the internal cable. Combined with slick coatings of inner cables offered with these cable systems, there is very little friction at that spot which would cause the rubber shield to move out of place during a release shift ( to a smaller, higher gear cog in the rear). The little feature on the end of the tongue effectively holds the rubber shield in place.
I have had these rubber shields migrate in a couple of instances. First, if the cap with tongue is excessively worn or damaged such that the little raised portion of the tongue is gone or damaged, the shield can more easily move out of position. Another situation was intense mountain bike riding where lots of vibration was occuring and the bike was moving through grass and weeds, I noticed the shield was out of place.
At any rate, you should not find the rubber shield to be migrating much, if at all. Correct placement where you have it will not effect shifting if it does happen to move out of position and that goes unnoticed for a ride. If the raised area of the tongue is intact, the rubber shield will be effectively locked in place in all but the most unusual conditions.