No, it was never a Second Amendment issue. It was a First Amendment issue. The NRA's ability to advocate for the Second was limited by campaign finance legislation. The new legislation doesn't do that because the NRA is exempted. It may limit other, smaller RKBA groups who don't have the political power of the NRA; but what does the NRA "owe" to those groups?
If the NRA opposes the legislation, then:
1. They irritate the Dem leadership which currently has large majorities in both houses.
2. They lose their exemption - meaning that if the legislation passes anyway they will be required to give up lobbying within 90 days of an election or disclose their membership list.
So what is in the best interest of the NRA membership?