Drive-by-Wire Throttle System?
 

can anyone explain what the drive-by-wire throttle system in the 09 manual accord coupe does? does it change the way the transmission works?

It can't change the way a manual tranny works.

On my Civic, it can make the AC just about perfectly seamless. When the AC compressor kicks in, it automatically opens the throttle just enough so you hardly feel anything. And no need for separate IAC FIT valves; that stuff is done just by the ECU directly operating the throttle.

I think on the R-series Civic engine the iVTEC messes with the valvegear to make a compression ratio lower than the expansion ratio (kinda like the Mazda "Miller cycle"). Ordinarily that would make a sudden sharp change in power, but the motorized throttle compensates so you don't feel it.