I mean, PWAs by definition run inside a VM that has to provide a very heavy runtime, don't they?
This isn't a (comparatively) minimal like the JVM -- this is usually a Chromium instance, with the full V8 engine, Canvas and DOM support, and sandboxing.
It's not reasonable to say that something with this much baggage should be able to run as quickly as a native application, which can often afford to have a much more minimal sandbox, no bytecode layer, a smaller memory footprint, and more deliberate and performant integration with underlying system APIs.