Signatures apply to the entire transaction. There are options to only sign part of the transaction, but by default all outputs are signed.
Alice.Bail.In can only be added to the blockchain exactly as written.
There is a weakness where Bob can spend Alice.Bail.In:1 without participating in the protocol. It is assumed that fees are low enough that it doesn't matter. If he does spend it, then he has to release x, so Alice can spend his fee on his Bail in.
Alice should not release her Bail-in until Bob does first.
and
Bob wants to spend Bob.Payout
He has a signed version of Bob.Payout input 0, signed by Alice.
He can add his own signature to that, and input zero is signed.
Alice's signature refers to the entire transaction except the input scripts. It DOES include the tx-id and index number.
Bob cannot change what input 1 refers to. He has to sign Alice.Bail.In:1. That requires he reveals x.