Yes the water remains in the tubes but you can flush them by blowing air on the last fill of the season.
Secondly, the tubes are small and flexible so they probably could deal with freezing very well. Here is what he instructions say:
For general winterizing, drain excess water in water supply line by pushing the spring loaded button on the end of the line. To remove the clear tubing (if necessary), pinch the tubing next to fitting, carefully twist and pull straight off.
Come to think of it, water came out of the overflow holes in the manifold when the valves closed to prevent over filling. I wonder if blowing air will push the water out the same way. I will try it this weekend and update.
2016 Georgetown 364 TSF
2015 FunFinder 242BDS traded for above
2014 Starcraft 1221 Comet traded for above