Few thoughts,
1. Long time ago i read Bitcoin Core doesn't implement BIP39 due to security issue[1], which isn't solved by your proposal.
2. If i understood your proposal correctly, does that mean 12 word mnemonic have less than 128-bit entropy due to version field addition?
[1]
https://bitcoin.stackexchange.com/a/88244[1] If the security issue you are referring to involves the use of PBKDF2, this could be addressed by implementing versioning, although it would break compatibility with non-versioned BIP39 software.
[2] Correct, a 128-bit entropy results in a 15-word mnemonic when considering the 24-bit general-purpose field is used.
For a 12-word mnemonic phrase under the versioned BIP39, you can attain a maximum of 120 bits of entropy, whereas the non-versioned BIP39 allows for 128 bits of entropy with a 12-word mnemonic.