Is it possible to submit a MathJobs application before a reference letter arrives? If I'm awaiting a reference letter, is it possible to send a MathJob application before the reference letter arrives? If I do this, will the employer be able get that reference letter whenever it is uploaded? Or should I not do this because the application would be submitted without the required letter?
Yes, this is possible. (At any rate, it was a few years ago -- I assume the software has not changed since then.) Hiring committees will be able to see whatever you have submitted, and once your reference writer submits your letter it will be visible with the rest of your application.