For MathJobs does it matter what you put down for Primary Interest?
When I, as a faculty member, go to MathJobs to evaluate postdoc applications, the first thing I do is to click a link that sorts the applications by research area. That way, I can efficiently go through the applications in my field without having to scroll through the whole database. As far as I can tell, the sorting is done on the basis of the applicant's primary interest. So the answer to your title is yes, your choice of primary interest definitely matters.