FWIW, I began Starting Strength doing the high-bar squat, because I didn't like the feel of low-bar. After my first reset (290), I decided to do low-bar. I finally got the hang of it and continued using low-bar ever since.
During that time, my deadlift did continue to move up. However, I noticed that before, when I was doing high-bar, I'd usually fail a deadlift because I didn't have enough strength to even get it off the ground, and the max effort ones I was able to lock out really took a lot out of me -- blood rushing to my head, seeing red & black, feeling like I wanted to vomit, etc. After switching to low-bar, failed deadlifts were more commonly due to a weak grip, whereas my body felt like it could have handled more punishment.
So to summarize, if you really want to maximize your deadlift, I'd recommend getting used to low-bar position. However, if you stick with high-bar squats, your deadlift will continue to go up, just at a slightly lower pace. Personally speaking, I'd rather just grin and bear it than load up the routine with extra pulls.