I found the source for TC_Configure() in the arduino dist (.../hardware/arduino/sam/system/libsam/{include/tc.h,source/tc.c}).
In this case, it appears that the ATMEL documentation and the code in the arduino dist do not match. The documentation for tc_init() appears to match the source code for TC_Configure (caveat: I just took a quick look, but it appears to be essentially the same function). My guess is that they renamed the function at some point, and that the docs and code diverged.
The source for TC_Configure is pretty clear if you also look at the SAM3X data sheet for the behavior of the TC registers.
Best,
Bruce