Given all that, if you were me, would you chose to wire your +5v power wire (from the supply board) to the VIN or to the +5v pin?
As mentioned and explained above, 5V into Vin WILL NOT WORK. You've tested yourself, that it doesn't work.
If I were you, I would probably connect the 5V from the supply board to a usb cable. In that case, you can either have the USB cable from the PC or from the supply board plugged in, but never both at the same time.
Another solution (but not so fail-safe) is to ALWAYS power the arduino from the supply board, even during software updates. For this, I have a specially modified USB cable, where I cut the +5V wire, so that the PC can not supply 5V to the arduino.
And to explain why 2 different 5V power supplies at the same time are bad:
It's got nothing to do with the 16u2 chip, or "original vs. clone"
These 2 power supplies will never be EXACTLY same voltage. One will always be a bit higher. It will "fight" against the lower one, by supplying ever more current to increase the voltage. In this process, one or both of the power supplies might get damaged.
Note: 7 volt into Vin is also a 5V power supply, because these 7V go into the onboard 5V regulator. If this regulator burns through, then you will have 7V on the board. This can surely damage the 16u2 chip - and of course also the atmega chip.
I hope this clarifies the issue a bit.
P.S. Since this is a recurring issue for newcomers, I wonder if it would have been a better design idea to have a switch or jumper on the arduino board, where the user can select from the 3 possible power sources. On the other hand... you would probably get countless people who think their arduino is dead, because they forgot to choose the correct power source.