I'm Sure if he was signed by any one else - he'd have a work permit by now
Doing a bit of accounting here.
As Nigeria are currently somewhere around 45th in the world, Onyekuru would have to have played in 75% of Nigeria's competitive fixtures in the last two years, for which he was available for selection. Let's see what those are:
2017 WC qualifiers - appeared in 1, not in squad for 3
2018 World Cup - not in squad for 3. Note that, while he was back in training following a bad knee injury, he had not appeared for Anderlecht and was not deemed ready for inclusion in Nigeria's squad. There could be some argument about whether he was truly "available for selection" for Nigeria here.
2018 AFCON qualifiers - appeared in 4 of 4 (he was a sub for the last few minutes in each, but they all count)
2019 AFCON qualifiers - played the full 90 and scored yesterday
We figure that the World Cup matches counted against him since he wasn't granted a work permit this past summer (being 21 this summer, only the last year of matches was looked at, so he would have only appeared in 1/7). So that's 6 of 12 matches now, or 50%. Africa Cup of Nations is this summer prior to the registration deadline, so that's a minimum of 3 and a maximum of 7 more matches. Even if Nigeria reaches the final (or third-place match), 13/19 is still just 68%, and Nigeria are a stretch to climb to 30th ranking so that the cutoff is 60%. If they do, they've likely won the tournament, so 6 appearances from 7 would do it.
So we go to points. Category A would give him likely give 2 points for wages in the top half of PL earners, plus 1 point for CL group stage participation. That's less than 4, so on to Category B. I'm guessing the transfer fee (7M or so) is probably in the 25-50th percentile, so 1 point. Turkey is a secondary league, so 1 point. Plus another 1 point if Nigeria reaches the AFCON semifinals. That gives him 5, perhaps 6 points, which is sufficient for consideration by the panel.
I would figure he'll qualify for a work permit this summer, especially if Nigeria performs well. If I'm wrong about the WC matches counting against him, then he'll qualify automatically so long as he plays in all the matches at AFCON.