I've found with my P2, I can have it lock onto the outboard clock, or I can set it to a specific clock and have it record/convert/whatever at that "rate".
I record digi-out from the TiVo's SPDIF all the time (VH1 is good for that). Sometimes, I record the 16/48 it puts out and go 16/48>16/44 with Audacity. Other times, I just set the recorder for 16/44 and record.
Seems to work just fine both ways, but I'm sure having the P2 resample something isn't a good idea. But who cares, I'm taping crap off the TiVo (Peter Griffin's "Can't Touch Me")...
Terry