The 5V on the USB cable simply connects to the 5V rail on the Arduino - its equivalent to directly powering the 5V pin.
I'm an IT guy not a electronics guy; so I don't dare to say you are wrong but the info you provide is seem conflicting to me with other info available.
When looking at he schematics http://arduino.cc/en/uploads/Main/Arduino_Uno_Rev3-schematic.pdf
I can not conclude Vin and USB power line are connected. I don't know what you mean with equivalent.
If the 5V and USB are connected I think I would have a problem when I connect my USB cable because then I would put my USB power in parallel to my switching regulator. In that case I would prefer to power my Arduino with a USB cable because I need to unplug it before plugging in a USB cable connected to my PC.
If they are not connected Arduino explicitly states that 5V does not go over the regulator so plugging in a USB must give problem when having power on 5V.
There is nothing wrong in powered the Arduino via the 5V pin - but you _must_ ensure it is a regulated 5V which never ever goes above 5.5V or so... If you have a cheap-and-cheerful "5V power supply" its up to you to verify it does actually put out a well-regulated 5V. You need to measure it with a multimeter under no load and under load (not your Arduino!) to check the DC output is 5.0V +/- 0.1V and that the AC component is small (< 50mV is advised).
These requirements seem tight to me. I don't think I can measure this with a multimeter. I guess you need a scope because you need to switch on and off devices to be sure there are no voltage drops and peaks.
PS I'm currently using a switching power regulator and a 100uf cap over it.
[Edit] Corrected the Vin pins to 5V pins