For the record it was never intended to be a 100% chance, this was an unfortunate error that I left in place while testing the functionality for I believe one of the Beta releases. If you are playing an official release version that has this error in place then I would suggest updating to the latest release version as it has since been corrected.
I've also just removed the ability of Transports to inflict damage as we agree with this oversight as well. As to changing the possibility of a unit receiving damage at less than 50%, or due to other factors, we are still thinking about it and would like to hear back from others as well before committing to any change.
One main reason is that as mentioned before, previously units could not pass through enemy units at all, and this also did not take into account readiness, strength, morale etc., and now players have a choice and you don't have to attempt to pass through an enemy unit if you prefer not to.
But with this new ability, we do feel that there needs to be some potential consequences of a cut and run through a line of enemy naval units, and even weakened enemy naval units could arguably have the chance to cause potential damage to a fleeing unit in this manner.
We'll continue to monitor this thread or any similar as we move forward and go from there,