Do you think it's that or they'd prefer to get their 30% cut of transactions?

I think it's that. Remember that Steve Jobs didn't want third party apps on the iPhone and had to be talked into it.

Steve Jobs is dead, and Apple's primary responsibility is to its shareholders, not its users. Subtly and pervasively hamstringing PWAs doesn't protect users. What would it even be protecting them from? PWAs that work well offline? No, it just coerces developers into writing native apps and distributing them through Apple's App Store instead.

While being locked in to a single app store without jailbreak isn't ideal, I'd rather have a native app on my phone than some lowest-bidder web app that downloads 10MB every time and runs terribly.

Right, the original story was write web apps. So Apple has changed tunes on this topic before.