I think one should do intersection calculations when layers are in the same coordinate system, and one should do area calculations in the appropriate projected coordinate system.
The order matters, but is one preferred? In my system, I get slightly different areas if I
1) Perform intersection of two layers that are in the same geographic coordinate systems, project the resulting intersection to a projected coordinate system, and then calculate areas, or
2) Project two layers to the same projected coordinate system, intersect them, and then calculate areas of the resulting intersection.
Without getting into details of my specific situation, I wonder if one of these approaches is theoretically preferable? I assume the 2nd would be, but I can't articulate why that would be.
(I assume terms are standard, but this is the intersection I'm looking for: http://wiki.gis.com/wiki/index.php/Intersect)