I think there's a lot of edge cases, and just spinning up an entire new data container for iOS Chrome and launching a web app inside it would probably make Chrome very confused. (It wouldn't know to hide its normal tab/browser UI, to not nag the user about logging into their google account, etc.)
Like I said, Apple could totally make APIs so that Chrome could know it was being launched in a container with data isolation and should behave as a web app. Google could then adopt those APIs, with the alacrity that it's famous for showing with new iOS system APIs. But the behavior Apple is implementing here is probably how any default-browser that hadn't yet opted into those new APIs would have to behave.
(To be clear: I think Apple is being petty here by not having those APIs announced. But "we're going to regress everything to bookmarks" is probably more DMA-compliant than "things are better when you use Safari, and we promise we'll extend that to other browsers someday".)
Currently Safari on Mac copies over login cookies and data directly relevant to the site and nothing else when installing an app as a PWA.
This strikes me as the way to go, there’s no good reason for anything else to be copied and it reduces the amount of data that integrated privacy-compromising ad and analytics services can readily glean from users.