I have just finished my initial proposal and I currently work on the motivation letter. The Politecnico di Milano deadline for Ph.D. is next Friday, May 29,2020. My referee and former supervisor is so quick, when I ask him to respond the email sent by universities, he responds within a few hours but I want to make sure that if it is possible if a referee send the recommendation letter 4 or 5 days after the deadline.
You should double-check the application instructions and if nothing is there, then call the admissions officer in the school. My guess is that there is not a problem, but it is better to be safe.
Often, this is not an issue. Referees are contacted via email by the university and they submit their applications themselves electronically, either by following a link or by email. The requirement for the application is usually limited to name the referees, not submit the references themselves. These days, it is uncommon for "sealed, stamped and signed" references in paper to be submitted, and including open references in applications is also not usual (although I have done so personally). I know it happens, though, but all in all reference submissions are often not bound by the same deadlines as the applications.
It is totally up to the school/department, so you should contact them.
For example, ETH Zurich does not accept any late submission, just out of principle, but many schools/departments accept late referee submission if they don't start processing the applications right after the deadline and behave more flexible.