Will water be an issue if I don't fix the cracked plastic between the back window and the trunk?

yes that is were most the water goes from run off either way you should have that sealed because it will cause moisture to build up in your car as well.

In my 2010 cc sport I did a test with spraying water into the same type of crack. It goes to the run off of the trunk but not INSIDE the trunk.

well if your in a snow area or have lots of blowing sand do you really want the snow and sand to go right into your car not to mention the hot air blowing in as well as cold air during the winter time.? the window is sealed for a reason its to keep the elements out of your car. Not to mention if you use your heater and ac it will all just casually flow out that spot in your window making your cars environ controls have to work harder to keep your car cool or warm. Having a partial seal will also run the risk of the window breaking twice as easy or even fall out over time.

That is a trim piece and it will not leak into your car. The new ones are metal. They break from body flex. The plastic doesn't flex and you get a crack. They are easy to replace and if your still under warrenty it is covered.

Dumb ASS nothing goes into or out of the car or trunk from this piece of trim. It is cosmetic only. There is a gasket that seals the car....