Transaction Malleability

I understand what transaction malleability is and how it is achieved but I don’t fully understand the consequences of it. Bob for example alters Alice’s signature data, hence altering the transaction identifier. What does this imply? That this transaction will be deemed invalid by the miner because the tx id has changed? This will result in Alice not being able to process future transactions depending on this UTXO, since it was never accepted by the miners. 
Or will it be accepted but under another tx id so Bob can say Alice’s transaction never came through? The transaction, however, remains untouched other than that the tx id has been tampered with? This would mean that the transaction will just be validated like any other transaction. What happens for future transactions when Alice wants to use this certain UTXO? Will it just use the altered tx id, or will this not be possible, since the tx id is wrong. In this case Alice will never be able to spend the UTXO?