If buying new from the shop, they really should swap the stem for you, especially at those prices. My shop swapped the stem and handlebar for me for free, though I supplied my own bars as they don't do exchanges on those.

​​​​​​At 5'9” I was between 54 and 56 on my Roubaix (2019 model year). I picked the 54 to have a lower position on the bike with the stem flipped, and replaced the Specialized Hover bar to lose even more effective stack. I've never regretted the choice, the only issue I've had choosing the smaller frame was toe overlap. I see how 54 could work for you if you leave the spacers maxed out and keep the Hover bar, but only you would know how upright is good enough for the position you're looking for.