I wouldn't sweat it. We're only talking about a 1,000 BTU difference between the two units. And it is a certified AHRI match. Also, it has a slightly better SEER rating as well. Maybe the contractor picked the AHRI match up with the highest SEER rating. Thats what I would do if the homes sizing calc could do without the extra 1k BTU and slightly less airflow. The airflow could also be a reason why he went with that air handler. I always make sure that the duct is capable of the full 4 tons of air, if its a bit shy the 3.5 is a perfect solution. Here is the AHRI reference # for both the GAM542 and the GAM548 to compare:
GAM542
4150838
http://www.ahridirectory.org/ahridir...ultSearch.aspx
GAM548
4150839
http://www.ahridirectory.org/ahridir...ultSearch.aspx
Honestly, he should have been able to tell you what I'm telling you though... Who knows what the motive was but all I'm sayin' is that you have an engineered match and its unlikely that you are going to see any kind of problem in my opinion.