I discovered https://github.com/requery/sqlite-android which builds with a recent version of SQLite along with a recent version of the AOSP SQLite database classes, and it seems to support 64-bit CPUs. It is apparently based on Android SQLite bindings at: https://www.sqlite.org/android/doc/trunk/www/index.wiki
Unfortunately I did not have a chance to experiment so much with it but I suspect a version could be used to provide SQLCipher with a number of recent AOSP features. I would recommend adapting it to pass as much of the existing SQLCipher for Android test suite as practical.
Yes it would be possible to adapt the current SQLCipher for Android source to support 64-bit native pointer values but then it would deviate even further from the AOSP code. That could potentially make it even harder to integrate newer features from AOSP in the future.
I hope this helps and apologize for the timing. I wish I had found it before you guys did the hard work to support Android N.