You don't need the bip39 option. In fact you shouldn't be using the bip39 option unless you are restoring another software's wallet in electrum. That is because electrum may drop support for bip39 in future.
I don't foresee Electrum dropping bip39 support in the future. Hardware wallets use bip39 so dropping support for this would also make the hardware wallets no longer function.
bi39 is the standard for seed mnemonics. When it comes to HW wallets the seed mnemonic stays in the HW wallet. It is only shown to the user on the display for backup purposes. Electrum never gets to handle it because that would defeat the purpose of using an HW wallet (private keys, such as those derived from a seed, remain on the HW wallet). So bip39 support is not required in order to support HW wallets.
You can see
here that ThomasV has said he can't guarantee bip39 support will always be there.
Sidenote: is there a decent link where I could study the math on just how secure the extend seed option would be at "hiding" a wallet. Is it basically the same math used by my Trezors in creating hidden wallets. Sounds identical. Love math, links?
You can see the code
here. It's running the mnemonic through a key derivation function. The custom words are used as salt. This is a function first proposed (ironically enough)
in the bip39 standard.