It's not clear if iMessage will interoperate via RCS, which is what would make blue/green bubbles less relevant. My assumption would be no as they'd cede moat, and there isn't much of a network effect for them to gain from.
Apple is not changing anything about how iMessage works, it's clear in their statement in the article you linked:
> We believe RCS Universal Profile will offer a better interoperability experience when compared to SMS or MMS. This will work alongside iMessage, which will continue to be the best and most secure messaging experience for Apple users.
It's not clear if iMessage will interoperate via RCS, which is what would make blue/green bubbles less relevant. My assumption would be no as they'd cede moat, and there isn't much of a network effect for them to gain from.