We'll soon be launching an WAB dev 1.3 app referencing a map on portal 10.3.1...I hope this isn't a bug.
Edit: We were working on one in v1.2, but since 1.3 was released, moved to that version. I can confirm though, that if the app was created using the WAB packaged with Portal 10.3.1, we didn't have any issues deploying it on a web server.