OK
The last post (https://forum.arduino.cc/t/error-avrdude-jtagmkii-initialize-cannot-locate-flash-and-boot-memories-in-description/1193800/3) indicates that AVRdude has been updated. Chances that Arduino will update the board package to accomodate a new AVRdude version are slim in my opinion; it might happen if Arduino decides design another board based on the 4809.
As you say, it's not a massive deal so I guess one has to learn to live with it.
I can't help you with the reset issue. Does this happen with basic examples as well?