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Why? Bag and baggage, the private keys only matter. Is there any essential difference in private keys generated from BIP39 SEED and native Electrum SEED?
There is no difference in private keys derived using any method as long as the method is cryptographically secure. As for the seed phrase itself apart from the BIP-32 seed derivation process, a very small difference in entropy size and the checksum there is no differences and these aren't really big differences either.
The procedure to create the legacy wallet via Electrum GUI is much easier than via its console and eliminates human errors.
I believe Electrum no longer lets you create a legacy wallet through the GUI.