It says "We do not guarantee that BIP39 imports will always be supported", which is a bit different to "They are likely to be deprecated". A very quick GitHub search says that message has been there for at least 2 years. Given how ubiquitous BIP39 seeds phrases are, I can't foresee the Electrum devs discontinuing support for them anytime soon.

That's not the issue in blue Snow's case, though. If you use an Electrum generated non-BIP39 seed, then the default derivation path is m/0, meaning the first address is m/0/0, which is neither of the derivation paths he ended up on above. Even if he had managed to import that seed phrase as a non-BIP39 phrase (which he can't, because Electrum won't accept it as a non-BIP39 phrase), then the addresses at the derivation paths we have discussed above would be different to the addresses obtained. He obtained addresses linked to the BIP39 phrase both in and out of Electrum, so he managed to import the seed phrase correctly. His issue is with using custom derivation paths, not with importing the seed phrase incorrectly.