Generally speaking, you'll get used to it-- or more accurately, acclimate yourself to it. My neck would get really sore when I first got a road bike, but these thousands of miles later, it takes a long day in the saddle to bring any of that soreness back. Mind you, my saddle-to-bar drop is closer to 7", so the adaptation came out pretty quickly. I did (and still do) zero exercises.
Oh, a lighter helmet can really help as well.
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