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None of these things are a flaw in hardware wallets. If you type your seed in to a random website, then you are going to lose your coins regardless of what wallet you are using. Good hardware wallets such as Ledger devices have some of the highest resistance to physical attacks of any wallet. Hardware wallets are also great to use with a couple of different passphrases, which provides the best possible protection against a $5 wrench attack.
It isn't actually matter of wallet. That is just an example. The main thing is if you're using a secure, reliable system such as hardware wallet or any other decent wallet in an unsecure way, you will lose everything. Hardware wallet is not panacea, it still require proper using.
While I agree with you that passphrase+seed phrase combination strengthens security in case of hacker's attack, I can't agree this method is able to protect from any wrench attacks. I have a hunch, the size of the wrench will be a more important factor than the size of the secret password.