If you want to share the app id (com.example.app), then I would compile 2 separate keys using the android tools. One for the apk with crosswalk, and the other for the apk without crosswalk.
Both can share com.example.app
1. unique android key + v0.1.0 (with Crosswalk)
2. unique android key + v0.2.0 (without Crosswalk)