Wow, that was a total guess in the dark Cygnus
The 232 port on the 1500, 2500, z1, z9, etc. (as well as almost every other high end commercial/consumer product) allows external control exactly as you surmised.
Standard Yamaha protocols are available on their website under downloads, but I don't believe they have the setup utility program available on their site. The setup program does allow setup, but I'm not sure that it really is any easier than their OSD and using YPAO. The plus is that you (or more accurately: a dealer) can use the program to copy your room settings onto a computer and store them. So, should the product ever get out of whack do to you totally being clueless as to how to use it, the dealer can just go back in and restore the system settings to what they were after it was properly set up.
More often this port is used for control of the receiver by control systems like Crestron & AMX. Full 2-way control (like what current FM station you are on, what the volume level is, what the current input and surround mode is, etc.) are available through this port. You want the main receiver on and turned to the DVD input? Just a few quick programming commands and you better believe the receiver will be exactly where it is supposed to be.
The GENERAL RS-232 codes for all the commands and the feedback responses are available at
www.yamaha.com in the customer support section I believe. Just a PDF or Excel file with a complete listing.
Very few manufacturers ever give software/firmware updates through RS-232, but if they were to release a software/firmware upgrade, this port would be the way to load it up.
Hyper Terminal could be used to test the codes, but really, Yamaha has a stand alone program that deals with your Com port automatically... But, if you were interested - Yamaha products use a straight through serial cable with 9600, 8, N, 1 as the settings. No RTS/CTS is necessary.