I think it only makes sense that when have more than one user profiles bound to Chrome, the first screen that should pop up when you start Chrome should be the one that prompts you to select a user.
Then it should only open the windows from that profile's previous session (or a new window for that session depending on your preferences) and nothing else.
After this initial process you should still be able to open a new window for another user profile and have the windows from the different profiles be open alongside, simultaneously.
But the point is that on startup you should choose a profile to start.
The current behaviour is problematic, at least in Mac OS, because there is no easy way to open user sessions independently from each other, like you can do in Windows with desktop shortcuts, and it kind defeats the purpose of having, say, a home profile and a work profile.