This causes a few other problems. For example I use Hangouts Chat (chat.google.com) on my Google Apps account, and I also have a personal gmail. Ever since the change I have to log out from my personal gmail to use Hangouts Chat, because it is looking at my Chrome account and telling me that I'm not part of the organization. I can't switch to the Google Apps account at all.
I use this feature heavily to separate different clients.
It's also the reason why Chrome/Chromium are now out of the question for personal use: Much to complicated to keep things separated.