Follow-up Comment #3, bug #40831 (project avrdude):
Looking over the source code, it appears the issue is that the USB endpoints
are already pre-filled by the upper tool layer:
(In STK500v2.c:)
pgm->fd.usb.rep = USBDEV_BULK_EP_READ_MKII;
pgm->fd.usb.wep = USBDEV_BULK_EP_WRITE_MKII;
That means the read endpoint heuristics inside usb_libusb.c will not trigger
for known Atmel tools, and the code will assume that the read endpoint is
always equal to the tool defaults. This breaks for LUFA programmers in libUSB
compatibility mode, as the read endpoint index is changed to 0x83 (but the
descriptors are otherwise identical).
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