I agree that the actual effect of 0.5mm or even a mm in shock length is minimal. However since the ride height is determined by the spring and spring collar setting shortening the shock (actually you shorten the piston rod) means that at the same ride height the piston will sit lower in the shock body. That could have an effect if the difference in length is sufficient and you compare a minimum rebound and maximum rebound shock setup.
Personally I have never truly felt the difference so I would not worry about it too much.