AIIMS and JIPMER seats will be filled through All India Counselling conducted by the DGHS on behalf of the NMC. While the information bulletin says this, it also says that Candidates from Jammu and Kashmir who wish to participate in All India Counselling need to submit a self declaration form. But there is a para in the information bulletin and it goes on to say:

"Candidates from the UT of J&K and Ladakh can appear in NEET (UG) 2020 for admission to Private Medical/Dental/Ayurveda/Siddha/Unani/Homeopathy Colleges or any Private/Deemed University and AFMC, AIIMS, JIPMER subject to the fulfilment of respective eligibility conditions."

So going by this, a Candidate from Jammu and Kashmir can apply for AIIMS and JIPMER without producing a self declaration form but need to fulfil the individual eligibility conditions of AIIMS and JIPMER. For any questions regarding this, NTA has given an email id where your questions can be answered. You can write to them at: aiqpmt-mcc@nic.in