The only purpose of the external 5V regulator is that in conjunction with other measures (including a metal enclosure for the Duet and shielded cables), it allows RepRapPro to claim CE compliance for completed printers. Most people using the Duet but not building RepRapPro kits use the on-board switching regulator instead.
I don't believe the switching regulator affects the thermistor readings. It does add noise to the Z probe reading though, which you can reduce by adding a pin header for the Z probe at the bottom of the board and running wires to it on the back. I described this in a post on the Ormerod forum last year. But it isn't really necessary, especially when using my differential IR Z probe.
Large delta printer [miscsolutions.wordpress.com], E3D tool changer, Robotdigg SCARA printer, Crane Quad and Ormerod
Disclosure: I design Duet electronics and work on RepRapFirmware, [duet3d.com].