Four centimeters too high? Are you certain that's the correct size bike for you? Maybe you need the 54 cm bike for your leg length.
Top tube length is not any better to judge a bike size by than is seat tube length. You need to consider stack height as well. And take all three of those things in consideration. Seat tube length being the least useful, IMO.
If you are getting a larger size than recommended because you are trying to minimize bar drop, then by reducing the seat post length sticking out above the top tube you might be making the bike not able to absorb some of the road bumps and more will be going into your butt to fatigue you on longer rides.
Emonda is a great bike and screams "ride me" more than any other model of Trek to me. But it's also made for a aggressive position. If you don't want that, I'd think you'd be better off with a different model of bike.