Your link is correct -- Apple recently added the ability to programmatically modify the contents of push notifications which would allow one to build E2E on top of APNS. Android has always processed notifications through intents, so it's always had this capability. Google is just providing a pre built solution that works for some use cases but this method was technically possible before.

Not sure what Signal does here particularly, but their FAQ claims it's not a problem. https://support.signal.org/hc/en-us/articles/217524107-Can-G...