Right now, iOS users can't as easily understand the difference between iMessage and SMS, and I think it would make what's happening clearer to users if the apps were separate.
If you opened the "SMS" app to get your sms 2fa codes and talk to android users, and your "iMessage" app separately to talk to iPhone users, it would make people less mad when they open their iMessage app to iMessage, and instead weirdly get green bubble SMS.
It would be like if when I installed the "firefox" app on iOS it instead installed "safari" and touching the "firefox" icon opened "safari", and didn't have any firefox addons. Oh weird, sorry, bad example.
The point is not that iMessage is better than whatsapp, it's not. The point is that iPhone users try to use iMessage, and right now apple's weird SMS integration with it makes them accidentally use SMS and get annoyed.