With BIP66, all parts of BIP62 should be fixed (except those where the malleability comes from ECDSA signatures, but those aren't relevant here as it's the sender who strives for the txid remaining the same and no one else could be affected).
I think the main issue would be if the forked alt has not updated its tx signing code (as the sender's txid could be changed without their knowledge).
By this I am referring to the low S values issue which I patched for CIYAM here: https://github.com/ciyam/ciyam/blob/master/src/crypto_keys.cpp#L531
Other than that I think that using P2SH (rather than the original multisig) is just a neater approach (it probably doesn't alter the workflow though).
But honestly, I don't expect too many of them to include needed features.
