The deadline to apply to programs and submit all your required documents (except reference letters/forms) is different than the reference document deadline for the R-1 first iteration. There is always 7 days in-between these deadlines.
The reason why there are different dates is to give the ability to programs to have access to applications earlier so they can start their review process. However, considering some applicants may still be in a November elective, hoping to obtain a reference, the reference letter deadline is a week later.
UG and PG deans agreed multiple years ago that this was the best solution to allow programs more time to review, without penalizing applicants.