I suspect Apple has internally discussed it and concluded that it would too likely be abused and result in a poor user experience.
Also, Apple deliberately does not like background connections for battery saving reasons which is why everyone is required to use their push service, meaning iOS maintains a single energy efficient connection instead of each app maintaining their own TCP connection which may have no regard for energy efficiency.
I acknowledge it's possible that they don't want to remove reasons for people to rather make native apps, but given the other reasons, it would not be my first guess.
I really wish Google would crack down on this between the Googlebot and Chrome. There's zero valid reason for a website to send a notification request without user action to initiate it. The Googlebot could record any unsolicited notification requests and negatively impact the ranking of those sites, it's a decent indicator of scammy sites to begin with. Not to mention blacklisting those sites from making a notification request to Chrome.
Chrome could also just watch for notification requests no differently than how popups are blocked already. I'm sick of the hordes of websites constantly spamming those requests. What's sad is that I'll frequently see other users actually accepting those requests and getting a barrage of ads that they don't understand how to stop. This isn't rocket science to fix.
I'd compromise on "Install" vs. "Install with Notifications" as two options when buying/downloading an app. But having to do any of the developer's administrative bullshit when I'm trying to use the app is disrepecting my time.
Otherwise I don't want to see that shit until I go into a "Settings -> Notification" menu and explicitly enable it. And never in a web browser.
The model of "user choice" has contributed more to the modern hostile computing environments of the past decade than maybe anything else. Users don't want choices, they want tools to help do what they want, not what mediatech/adtech/social garbage app firms think they should want. Mostly, users want their computers to shut the fuck up and get out of the way.
If Apple doesn't allow PWA to use notifications (current situation), then neither the developer or you as a user have a choice.
Guess which one is best for the users overall? Guess which one is best for Apple overall?