Usually if the school lists a single application due date, that's when they want all the materials by. I've never heard of schools not sending LOR info until the application is submitted--usually the emails are sent when you register your recommenders.
Often they list two dates, one for your application and one for supplementary materials, in which case of course the LORs would need to be in by the latter date.
If you actually have a school that doesn't send out LOR requests until you submit the app and all they list is the application deadline, then I can't imagine they'd expect the LORs by that date as well. The easiest thing for you to do in this case is give the department a call and ask. You can have this cleared up 100% in five minutes.
Seems like every university has their own way of doing this
but here is what I found in cornells application
Online submission note:
After entering the recommender's information below, you may also need to register each online recommender in the Recommender section of this application. Please note that Recommenders for applicants in the following fields will not be notified until AFTER their application has been submitted
and applied physics is one of those fields. But if application deadline is Jan 5 (which it is for cornell) then how would recommendations work if i submitted on jan 5? I guess I could call each school