The BIP32 Extended Keys are different?
Because they are doing two different things.

libbitcoin is taking the entropy and directly using it as a BIP 32 seed to produce the BIP 32 master private key.

However the web based wallet is taking the entropy, producing a BIP 39 mnemonic, then using the BIP 39 mnemonic to produce the BIP 32 seed and from there the master private key. Since BIP 39 mnemonic to BIP 32 seed involves hashes and does not result in the same value used to create the mnemonic, the resulting BIP 32 seed is different from your initial entropy. Thus you are getting two different private keys.