No, I don't. Don't get me wrong. I believe that using an electrum seed is better than a BIP39 one. But, for the non-code experts, or the people who simply don't look into the code, generating a seed that can only be used by one software may not attract them that much. They will consider this a downside.
Hmm, not really sure if that really matters actually. I don't recommend people to start mixing seeds or start to use seeds interchangably. Perhaps there could be some utility to help people recover Electrum seeds? Definitely not a deal breaker but the point is, if you're going to use Electrum, just might as well generate a seed that uses Electrum's standards. Even if it were to be abandoned in the future, I'm confident to say that there will either be a utility to convert it to a BIP32 seed or users can just transfer it out somehow.
I would definitely be sure that BIP39 will eventually be abandoned at some point in time, or at least wallets will start adopting a different standards for mnemonic.
4.0.4. Have they changed it since then?
Yes they have. I think it has been like this since 4.1.0.