There is one backlight effect option called "Colourtime" that sets each LED's color individually based on the number being displayed on each tube. E.g. if a tube is displaying 0 its LED would be red but if it's displaying 1 the LED would be yellow, etc. This would look rather strange with the LEDs out of order because the LED associated with the seconds tube changes rapidly and so on.
If you really need to mount the LEDs out of order changing the code accordingly shouldn't be very difficult for you.
Another thing to consider is that if the new kits (DA-2000) the LED colors are used to indicate progress of the power up / self test sequence. If this feature is added to the Classic firmware some day, having the LEDs mounted out of order would make that sequence look wrong.
Look into it later when the dust is clearing off the crater.