Dustin,
In theory, assuming both arrows are the same weight and shot from the same bow, the trajectory will be identical. But the one variable that is more difficult to quantify is the efficiency of energy transfer from the bow to the arrow. With our two identical wt. arrows, if one is 100% efficient and the other is 80% then the first arrow should have a better trajectory. One of the significant parameters in obtaining more efficiency is reducing the amplitude of the oscellations called archer's paradox. Increasing the FOC on a perfectly spined shaft is one way, adding 5 1/2" fletching is another. Obviously increasing the size of the fletching, while reducing the amplitude of oscellations also robs the efficient transfer of energy.
Ideally, a perfect arrow will have all the wt. up front and no fletching but that is impractical even for target uses. So, we compromise by adding enough fletching to stabilize broadheads in adverse conditions while maintaining the highest transfer of energy efficiency.
In my case I have gravitated to an arrow of 645 grains and 31.6% FOC that flies like a laser even with big Grizzly Kodiak broadheads.
It's all about tuning but there is way more to it than many people realize.