I'm not sure the Electrum dev team think their seeds are "better," but are they?
They do. BIP39 was also marked as discouraged for implementation.
They still use the same word list, and I imagine the provide the same level of entropy as a bip39 seeds for given phrase length. I thought the re-configured checksums of Electrum seeds are only meant to allow the phrase to define the type of wallet it creates, ie segwit vs legacy. Is there more to it than that?
The version bytes are defined at the start. Checksum has nothing to do with the type of seed it was meant to be. Electrum seeds doesn't require a fixed word list.
Trezor's SatoshiLabs were involved with BIP39 development. I don't think it's impossible to implement something like this in their firmware but there isn't any problems with security or anything that urgent which would require something like this.
While there's still a small chance that an Electrum seed is a valid BIP39 seed as well, Electrum will ensure that they won't inadvertently generate valid one that is compatible with both in the new release.