SE has been known to skip minor details, usually on accident.
It's possible that they're removing it from the KS99 too, but it's also possible they'll remain.
Even assuming so, my group just did 5 or 6 turtle KSNMs the other day and didn't get the BB item. Plus, we also kinda wasted seals now that this system will be in place and we'll no longer be able to camp the real turtle.
Another thing to note is that we aren't sure what the drop rate of the pop items are. For all we know we could blow 99 KSs and not get one. Or we could blow them, get one pop, kill the NQ, not get an HQ pop. Same route, and HQ doesn't drop the BB item.
Overall they tried to fix a problem and caused another one. They should have left it alone.