If you are configuring Guided Setup to work with the two external boxes then yes the TiVo sends the IR codes for both boxes.
Two things to remember:
1. You will need the 2nd A/V mod so that the TiVo can accept both STB inputs
2. You will also need a dual-head IR Blaster emitter and place one head in front of the digital STB and the other in front of the Foxtel box.
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