In my neighborhood, for example, it's rare for houses to be renovated fully permitted because the entire permitting process is designed around large scale construction projects. There's an entire shadow economy that goes just to paying thousands to architects, expediters, inspectors, licensed pros, etc., in addition to the actual work. That's just one example. The end result is that people don't do it, because they can't afford it unless they have a lot of capital.
Now the law already does this distinction I'm mentioning: for example a three or four family home has to be registered for the rentals to be legal, a two-family doesn't. Also the code is different, and more broadly the Multiple Dwelling Law treats them differently.
Going back to AirBNB, concretely I think a good compromise would be to limit the number of units for rent to one, and take down the ones that have turned rental buildings into hotels. People who own big rental buildings do these things. What's left are co-ops and condos. Co-ops have self-regulating powers to evict people. Condos, which someone here complained upon, are a different story (even if they have house rules with fines, I don't know how that's enforced).
The 'knocking on the door' comment was an attempt to try to separate the large from the small. As for myself I'm always above board and legal, because I'm risk-averse, but my risk-averse nature also means I don't rent to anyone I don't know or trust. Partly because of comments about everyone needing sticks. Ironically I've been on that side, which is why I decided I didn't like being a tenant anymore. I haven't used AirBNB, but plan to do so -legally. I do have a right to feel wronged by the passage of the law, especially when I hear all the anti-AirBNB comments not apply to my situation (eg. 'disruption to the residents').
The idea that tenants are able to knock on your door means you shouldn't have to follow this law kind of demonstrates an attitude I've seen with a number of small but not "good" landlords I've had.