i don't think it is possible in FCP.
(this is one of those "i'd be glad to be proven wrong" statements)
i do believe there is an app that will put the aux TC track into the TC track as a batch operation.
so you could media manage the program,
swap the TC for the Aux TC on the copied media,
then Batch Capture.
(later)
maybe i'm just imagining this app exists?
i believe i had "Multiclip Off-setter" in mind,
this comes from David Heidelberger
[
www.davidheidelberger.com]
you could ask over at Video Toolshed, or Spherico Filmtools too.
nick