I need to power the DUE with its 5V Pin in normal operation. What are the side effects of this?
Is there any component used in an unspecified range?
I guess one should also avoid connecting the DUE to USB while having the 5V supplied at the 5V pin.
Is there a suggested modification to the board?
The only thing I can think of is that you will have trouble powering up attached peripherals, but that depends on how many peripherals you have attached to the board and how much current(?) they need to draw from the board. So, if you can power as many as possible peripherals from external power supplies, this way you don't use the Due to power them, then you should be fine.