The 29 June Federal Register page is an amendment to SFAR 118. So the policy has changed. The problem was if everyone was extended to 30 June you would have 4 months of pilot medicals expiring at the same time. The current rule says -
“To provide relief to those airmen who continue to be affected by restrictions and recommendations implementing phased reopening, and allow for flexibility in scheduling the medical exams, the FAA is amending the relief in SFAR 118. The FAA has determined that pilots may operate with a medical certificate that has been extended no more than 3 calendar months for a limited time without creating a risk to aviation safety that is unacceptable under the extraordinary circumstances surrounding the COVID-19 public health emergency. For the reasons cited, this final rule revises SFAR 118 to extend the validity period of medical certificates that expire in April through September 2020 to 3 calendar months beyond the original expiration. Accordingly, those pilots who obtained only a one- or two-month extension under the original SFAR will be granted additional relief not to exceed an extension of three months total. Those pilots who hold medical certificates that would have expired in March 2020 obtain no additional relief under this SFAR, and they must obtain a new medical certificate to continue operating after June 30, 2020. Pilots who hold medical certificates that expire in July, August, and September will have a full three-month extension.”
The bolding is mine but basically everyone gets an extra 3 months maximum.