Thanks chateauheart. This is sober but necessary advice. That said, given the rate at which academic publishing proceeds, maybe this will be done by the time I go on the job market...
This may seem unfair, because typically a working paper has a similar level of intellectual content as the final peer-reviewed article (in fact, some people think their papers were better before the peer review process). But this is just how academic signaling works. Without peer review, adcoms can't distinguish the paper's quality from any other paper, except for the words of your letter writer. So yes, it will be letter that counts.
Also, word of caution: judging from personal experience and some of the posts I've seen here, it seems common for professors to tell their RAs that their project may end up in a top 5 or top field journal. At a much higher frequency than is warranted. Some of this may be naive optimism. But do note that the professors benefit from your willingness to continue work on the paper and not let it go unpublished. So, until and unless the paper is published, you should always maintain an independent judgment on whether the project is actually going somewhere and worth spending more (unpaid) time to present/edit.
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