Short answer is "yes", custom arrows vs. what we used to call "barrel arrows" (as in, "arrers are over there in thet barrel fer 69¢ each") will be noticably better. BUT, a bad bow set-up will throw good and bad arrow poorly.
I enjoy making up cedar arrows and am willing to sacrifice some accuracy because I like everything about cedar arrows. Just my odd tastes.
By shooting bare shafts (points, but no fletch) at a piece of paper hung in a frame and observing the shape of the tears you can tune the bow. You can do the same, mostly, shooting at a target from a short distance and seeing how the nocks align with eth tips.