Applying for two Assistant Professor job posts on different subjects, but very related
Assuming both jobs are in the same department: Ask the contact person. (If that contact person won't be on the hiring committee, then get in contact with someone who is.)
Assuming both jobs are in different departments: (IMO) Departments are independent and two applications will not overlap at the department level. (They will, of course, overlap within the university.) I see no reason not to apply for both.
(Traditionally, this would have been easy: You'd write two applications, put them inside two envelopes, and put both envelopes inside a third along with an extra covering letter explaining that you're applying for both positions. You could even mention in both applications that you're applying for both positions. These days, with automated systems, this might not be possible. Depending on the system you're being forced to use, perhaps you can manage something along these lines.)