with my experience, as long as the fit is in the ballpark, your body will become used to the set up. No matter what, once you hop on your new bike it will feel weird. But, I currently have a 110x10ºx31.8 stem I am trying to switch out for a 80 or 90mmx0º stem. In theory its a fair difference, but im sure after a couple rides ill be alright.

You can always add or subtract spacers, flip stem, adjust bars, adjust seat, etc.