The reason the pins are mirrored is that it makes every line flow in parallel. And if you use a flat cable to crimp the RJ12 headers you wont get a twist between KCeptors.
The only precaution you have to follow is to also mirror the wires when crimping.
Here's a picture of both ends of a single Flat cable:
The RJ-11 connector was really useful while prototyping the system, and we are still using it. But the idea is to look for an alternative to be used on future releases. Take a look at this thread.
The resistors you mentioned are pull-ups for the i2c buses. Devices working with that bus are open drain: they can drive the line low, but cannot pull it high.
The Chordata Hub is basically a multiplexer outputting 6 i2c pairs, and each of those needs its own pull-up.
Same thing happens with R1 and R2 on the KC, they are pulling up the bus after the address translator. R3 is just to drive high some pins on the IMU.