No it has nothing to do with the WWOR's NJ License.
Even though "New Fox" & "News Corp." are two separate companies, both are still controlled by the Murdochs.
When Pai eliminated the Newspaper-Broadcast Cross-Ownership (NBCO) rule (part of that dereg rule he had in 2017), the Murdochs didn't need to ask for a waiver. But when the Third Circuit vacated & remand Pai's dereg measure in the fall of 2019, it reinstated the NBCO rule, thus them asking for a permanent waiver this time.
Even though it already had a permanent waiver to keep the Post & WNYW (since 1993), it didn't have one for The Post & WWOR, even though it granted them temporary waivers on three occasions (2001, 2006 & 2014).
I guess the reason why they gave them this temp waiver this time, they're basically saying lets wait until the outcome of the media ownership case in the Supreme Court. So for example, if SCOTUS rule that the NBCO stays, then the temporary waiver will stay active for 180 days after ruling. If its the other way around and they rule NBCO no longer needed, then the Murdochs would keep Fox 5, My 9 & the Post.
Pai could've easily granted them a permanent waiver. But I think he's banking on a Republican-controlled SCOTUS to rule in their favor so the court can put an end to the NBCO once and for all.