Resetting 16U2 Processor on Uno (R3)
What I think is happening here is that the HWBE fuse is set (hardware boot enable).

From the datasheet: 


  The Hardware Boot Enable Fuse (HWBE) can be programmed so that upon
  special hardware conditions under reset, the bootloader execution is forced after reset.


What this means is that under normal booting (power-on reset) the bootloader is not entered, and the device immediately identifies as a TTY device (ttyACM0) as you saw:

[ 6329.384088] cdc_acm 1-1.3:1.0: ttyACM0: USB ACM device


However if you manually reset it, it enters DFU mode with its bootloader, so you can reprogram the main code. Thus it identifies differently:

[ 6278.684841] usb 1-1.3: Product: ATmega16U2 DFU


Thus, a forced reset via the Reset pin acts differently to a power-on rest. By design.



If you search for uno enter dfu mode you will get quite a few hits. People use that technique to reprogram their ATmega16U2 (eg. to act as a MIDI interface).