I don't see how that could work in tup or any deterministic build system. If there is any possible way to parameterize explicit filenames unique to the stages, that will map better to tup. It requires you to be explicit about every file generated, even temp files. I've searched the mailing list for a few scenarios and the response is often to wrap tup in a makefile.

IIRC at least miktex came with a script that runs latex as often as needed until cross-references are resolved and the output is stable.

Instead of plugging latex directly into a Makefile or tup, use such a wrapper.

It seems that latexmk could be such a script: http://mirror.unl.edu/ctan/support/latexmk/README