USB to serial AVR chip code should be tweaked to use RTS
If we're going to fiddle with the 8u2 and "arduino" programmer type in avrdude, I'd like to get away from using rs232 signals at all. I think PaulS suggested picking a rare and uncommon bitrate, and resetting the Arduino AVR when that was set.
OTOH, "backward compatibility with 500,000 existing Arduinos..."
what is it about UNO in particular?
Different and Dumber bootloader, running at a different bitrate. Possibly a newer version of Avrdude in newer IDE releases.
Prior to Uno, the Bootloader would exit quickly when it saw "illegal" commands. The Uno bootloader isn't smart enough to check for illegal commands (although the most recent version can check for improperly received commands, as "probably" occur when commands are received at the wrong speed.)