I smell confusion.
you have to differenciate between the operation of the modchip and the programming of the modchip.
you can program the atmel either with serial or parallel or JTAG interface... you can use whatever you have.
when the modchip is in operation, it works as JTAG client and applies the memory patching via JTAG.
there is no "passthrough" because it is not needed.
if you want to dump the flashrom, you need to access the SMP863x JTAG interface from the PC, but in this case you have to remove
the modchip.
again, you can use whatever JTAG cable you have to do this, but you also need a software that supports MIPS CPUs.
the dump tool that we supply here only works with the cables shown in the WIKI.