Got an answer from google dev. In my case, a .bc file forced the 64-bit apk to run in 32-bit. So any apk with a .bc file will be treated as if it’s 32-bit, no matter what .so files it contains (or not).
It was the natcorder.bc file in my case. An update from Natcorder 1.3 => 1.6 should fix it ( NatCorder - Video Recording API page-34).
By the way, this seems to output more detailed error messages: bundletool | Android Studio | Android Developers.