I'm in the process of getting a road bike with the intention to use it for getting fit. I'm tried 2 Trek Emonda bikes yesterday at a LBS, one was a 56 and the other was 58. 

Honestly, after riding both of them, I could not determine which one felt better. The guy who was helping me out made me stand over both and both of them had plenty of space over the frame. He also said, that I could choose either one as my dimensions are in between these models, I'm 6' 1.

My question is, If I go with the 56, and if it happens to be the wrong size, what is going to be the long term consequence. Also, appreciate if you could answer the question the other way around?

If it ends up being the wrong size, would I be able to mitigate the consequences by modifying some other components later on?