Hello GuinnessTrinker,
CLK3 -> 50 MHz - LVDS18, this clock wont change in the near future. With the new Revision 03 of TE0712 the Si5338 does not even have to be programmed in your design. With revision 03 the default frequencies are like the programmed frequencies on revision 1 and 2.
We updated the table:
https://wiki.trenz-electronic.de/display/PD/TE0712+TRMIf ure using a Rev01 or Rev02 Module and dont want to configure the SI5338, you will only have the Clocks CLK1A, CLK2 and CLK3.
For sys_diff_clock to be 100MHz is wrong, thats a mistake, either set by vivado per default or just mistakenly put in. It is actually 50MHz. Important is, that 50MHz is set in the MIG IP, which it is at the "Memory Options" -> "Input Clock Period".