I don't think any of these are real weaknesses of BIP39. Points 1 through 4 are essentially "You lose access to it by some means or other". This is entirely preventable by making multiple back ups, and one of your back ups being stolen won't immediately lead to loss of your coins as long as you are using a long and random passphrase. Point 5 is easily negated by storing it in a way that TSA agents don't know what it is, or memorizing the 12 seeds for the brief duration of crossing the border. Points 6 and 7 are nothing to do with BIP39, but to do with the Trezor wallet, and are entirely negated by using a passphrase.
What you are suggesting is essentially a brainwallet. We obviously can't stop you from using one, but there is a reason that every serious user of bitcoin thinks that brainwallets are a terrible idea. BIP39 was specifically created to be a secure and easy to use method of backing up your coins.
That's a garbage site, I entered "11111111111111111111" and it said it's "reasonable".
The flaw with that site is that if you enter a single number (such as 1), it assumes you are using all numerical digits and adds 10 to your character set. If you enter a single lowercase or uppercase letter, it adds 26 (or 52 if you use both) to your character set. Same idea for symbols.
This approach makes sense if your password or passphrase is truly random. It doesn't make sense if your password is something you have picked yourself and isn't random, such as a password based on a phrase with some substituted characters, as OP has done, or if you use a repeating digit as you have done. Both these passphrases are not as secure as that site makes them out to be.