Should Ethernet MDI Pairs all be Length Matched (Inter-Pair) before going into magnetics?
There is no need to have the pair lengths balanced.
The standard for 1000base-T (IEEE Std 802.3-2008) states: 


  40.7.4.2 Link delay skew 
  
  The difference in propagation delay, or skew, between all duplex channel pair combinations of a link segment,
  under all conditions, shall not exceed 50 ns


So, 100 mil difference are no issue at all. In fact, even normal RJ-45 cables are not balanced on purpose: Each of the pairs usually has a different number of turn on the twisted pairs to reduce the amount of cross-talk. Over the length of dozens of meters, this can accumulate to some difference in the length of the pairs that is larger than the difference in trace length on your PCB.