Q: I own a PRS McCarty with Duncan Soapbar pickups (I dig the vintage vibe) and play through a Marshall Combo amp with one 12-inch speaker. I'm happy with my sound for the most part, but have two questions. The first is why my rhythm guitarist, who is playing through an older 4x10" Fender amp, is seemingly a lot louder than me, despite the fact that both our amps are rated at 40 watts.
A: Your first question isn't easily answered. For one thing, wattage doesn't equate directly to volume. There is also the question of "apparent" volume. A distorted tone may sound louder or quieter than a clean tone, even if both are at exactly the same sound pressure level. A brighter tone may cut through and sound louder.
Plus, there are many variables that can affect how loud an amp is for a given wattage. For example, you both have 40-watt amps, but one is projecting the sound out through a single 12-inch speaker, while the other is driving four 10-inch drivers, which is a lot more surface area. In general, more speakers will fill a room with sound more efficiently than a single speaker. Plus, different speakers have different efficiencies, different size cabinets project differently, the impedance each amp sees could be different, some amps seem to punch louder than others, and so on - there could be many factors involved.
You might talk to your Sales Engineer to see if there is a separate cabinet you can add on to "move more air" which translates to the impression of greater volume and typically a richer, fuller sound.