Why is it necessary to isolate MCU from the PoE part of the board?
The PoE side is an isolated module that you want to keep separate from your internal logic. 

There are a number of reasons why, but most importantly.


You do not want pass logic noise from your digital side to the Ethernet side.


If the PoE were connected to your logic ground you may pass significant noise out onto the Ethernet cables disrupting transmission bandwidth.


You do not want extraneous voltage events that may occur in the Ethernet cables propagating to your logic side.
When your logic side is turned off the PoE side wont be. Isolation helps prevent the PoE from trying to power up your logic through IO pins.