Can we use the some startup id logic that handles launching on correct display?

Are you referring to https://chromium-review.googlesource.com/c/chromium/src/+/1070711? I don't think that would be sufficient because we'd need to handle windows popping up not associated with the user launching from crOS, e.g. chat clients or other programs that will receive notifications.

If a new window is associated with an existing app then it will have properties set that will allow you to detect that. Either it's a transient of another window or the app/startup id will be set.

We can also expose the peer credentials of the connection if you're looking for a reliable trusted way to determine where a window comes from. This would give us the crosvm pid in our case. 

 Issue 849896  has been merged into this issue.

I tried to reproduce but got another result.
1) Logon with account A.
2) Sign in another account B.
3) Switch back to account A.
4) Click to start a Crostini app.
5) A spinner appears and wait for the container to start up.
6) Hurry up and switch to account B before the app starts.
7) The spinner appears on the shelf.
8) Then Chrome crashes.

With the tip of tree chrome build, chrome crashes when I try to do step 2) sign in another account B. The login screen shows and immediately crashes and back to account A.