The R565 is essentially a 105-grade crankset (maybe closer to Tiagra today, but 105 a couple years ago), and if I were upgrading I would definitely go to the FC-6800 as others have done to consider it a partial upgrade along the way to a future 11-speed setup. Bearings should match up perfectly so there should be no issues. Just make sure you re-use any spacers or bearing covers the same way as what you take off.
Also, assuming it's the BB90 bottom (forgot if you mentioned what year Madone 4.5), put the drive side bearing onto the crank first, not into the frame first. The final inch or so onto the crank tube is likely to be tight, and you don't want to put the pressure of getting those together onto the frame itself.
I'm intrigued if anyone has weighed the R565 against a labeled 105 crankset. I bought a "new" R700 crankset (apparently Ultegra comparable) when I changed a R553 triple to double and also needed to move to shorter crank arms, and you could definitely tell the difference in weight. The non-named Shimano R-series are pretty good, just not as pretty and definitely not as expensive as the named-series equivalents.
Last edited by JamesInSJ; 10-10-14 at 11:19 AM.