Roger's service has more pronounced pronation and he spends a higher percentage of the service energy on the dominant (=right) side of the body than Andy. Over his entire career on the tour (data until mid-January 2017), Federer has the 1st service percentage of 62% (Murray 58%, Djokovic 65%, Nadal 69%) on which he won 77% of the points (Murray 75%, Djokovic 73%, Nadal 72%)...
The above numbers tell us that Andy's service margins are mostly (besides aces) quite below the ones of his closest competitors. It's mainly his excellent return and rally game that make him to such a successful player he is. From the technical point of view, as I personally see it, a limited pronation and a rather unclear distinction between the follow through 1 and follow through 2 are the reasons behind Andy's lower service margins. Interestingly enough, Ivan Lendl (1st serve 56%, overall service points won 66%) had similar issues in his career.
