Bob does not broadcast the refund at start as it would not be included to the block chain or mem pool until its time has come.

The point of micropayment channell is not to broadcast anything but the final version of the settlement transaction.

The payee can flush the latest version of the settlement transaction any time to the block chain which then double spends and thereby invalidates
the refund. If this happens long before the refund timeout then malleability is not a concern.

The payer signs new versions of the settlement transaction and sends them to payee. Payer can not broadcast them as they are only signed by payer.
The payee will sign and broadcast the most favorable to him and that is the regular close of the channel.