Malleability affects pre-signed child transactions in chains of unconfirmed transactions.  If you malleate the parent transaction, the child transactions is not valid, anymore. These unconfirmed transaction chains are used in LN to securely open channels or close channels.

SegWit is also useful to pre-sign the child transaction before signing the parent transactions, e.g. for the initial funding transaction you want to have signed emergency close channel transactions before signing the funding transactions.  With SegWit the transaction id does not depend on the signature and can be computed before the funding transaction is signed.