JC,
The problem we are getting into here is mixing apples and grapes to some extent.
In your example the with the shafts being the same with a different sized fletching. Yes, they will drift at the same rate. However, the arrow with the most drag(larger fletch) will weathervane or windcock first given enough time airborne to become more streamlined.
On the second part about the same boats with different sized sails, you now have powered craft which changes things. Yes, the boat with the larger sail should out run the boat with the smaller sail. Remember that the boats would now be under windpower and would be generally steered to a course. Its now an issue of how much power(sail area)and controlling the sail.
This is different than a projectile being launched into free flight like an arrow given an initial trajectory no additional imputs other than wind factors.
This can get more complicated if you take the senerio of both boats not being steered but just drifting. Then you have several factors involved, the current of the water and the direction of the wind which would probably be different. The boat with the greater sail area would drift faster because of the larger sail area given hulls drag in the water would be equal. The direction of drift of each boat would probably be somewhat different because of the resulting vector from the two currents and the difference of the sail areas.
YIKES my head hurts!
