[Mark McLeod]

Tying the cables together securely is one reason.

The two ports on the OpenMesh are also setup differently, for instance the Open Mesh should be configured through the 802 port while the POE port handles power input.
From Beta testing and other Beta reports the POE port seemed to be less prone to roboRIO connection issues like the one's in some of the current CD threads.

In general, I recommend following FIRST's instructions, since they might add adaptations to the firmware, get all the bug reports, do their own confirmation testing, as well as have the manufacturers ear.
But if you encounter repetitive issues with one port, try the other.
Approximately one percent (made up statistic) of the radios might suffer from manufacturing oddities that benefit from wiring that one percent differently than what may be the standard FRC practice.