Previously, Safari handled these requirements because it's a modern browser (isolated storage has been a cornerstone of browser security for a long time), and had special privileges in iOS to configure per-site user permissions, whereas normal apps only had app-wide permissions.
Luckily, Chrome already has isolated per-site storage because it's also a modern browser. If it didn't, the world would probably explode.
That leaves per-site permissions as the only real problem. I'm sure the Chrome-on-iOS team would do whatever it takes to make this a good user experience, but let's assume for the sake of argument that this would actually be a burden for Apple to support.
How does disabling PWA functionality change the security situation whatsoever? Users preferring Chrome would just load the sites in Chrome as a bookmark, which has no meaningful difference from a "security" perspective. Users strictly using Safari obviously have a strictly-worse experience. Who does this help? What is made more secure by disabling this?