What happens in Star Trek is neither here or there in this debate.
Anyway, the Bird of Prey's weapons went through the shields, they penetrated, they didn't go around the shield.
Bypass would be an incorrect use of the word.
Matching frequencies doesn't make the shield anything other than what it was when it was raised, it actually changes the shields surround a torpedo or alters the energy of the energy weapons to be the same as that of the shields, hense they go through.
Matching frequencies wouldn't even be making a passage through the shield, it would be making the weapon the same as the shield your attacking.