AVRDUDE read options (flash, fuses) not dumping all data out to file

The Arduino bootloaders all (well, Optiboot, anyway) time out relatively quickly and execute the user sketch. This means that the "interactive" (-t) mode of avrdude is essentially useless for poking at them.

I'm not sure about your USBasp problems. Some of the inexpensive firmware for those progammers has trouble with the parts having more than 128k of flash, I think.