It is mandatory for an employer employing more than 2o employees to register itself with the EPFO. However, pursuant to a change in December, 2016, an employee's contribution to the EPF scheme has become optional (choice of the employee). An employee can chose to EITHER not contribute at all OR increase his percentage of contribution (up to the whole base salary amount)- as he/ she wishes.
Since the employee is adding the EPF equivalent to your monthly remuneration, my guess is that a claim of PF at the time of resignation would be denied/deemed redundant. As such, I believe the best and simplest idea would be to seek clarification of your doubts from your employer.
Lastly, as I often suggest, please run a relevant search on this website or www.citehr.com to make use of an abundant base of information readily available. For example-
From India , Delhi