Rheem vs. Amana
Recently had a 95% furnance installed. As I worked with the installer trying to find the best way to vent the system, he gave me the impresion that codes (or installer instructions) require 1' free space around the vent (i.e. must be at least 12" above the ground, and 12" below anything above it).
Unless you have a high ceiling, coming out under the deck will likely be within 12" of the bottom of the deck joists. And even if I'm wrong and code allows for less than 12", do you really want to vent under a deck? The exhaust isn't hot, but it is warm and moist. As such, when it comes out the vent, it's going to rise and send all that moisture to the underside of the deck.
Otherwise, you've already pointed out what I learned when I was researching furnaces... the installer is more important than the equipment. I've also heard that all the manufacturers use the same core components (i.e. everyone uses the same compressor, the difference is what they surround it with).