I guess I'm not quite sure of the problem here. One of your premises I believe isn't true:

"""
If the Gerrit account is linked both to chromium.org and webrtc.org accounts (and google.com in my case), it seems like the preferred Email at CL upload time decides the e-mail identity used for the CL.
"""

This is not true. Whatever the user has configured in their local "git config user.email" is what determines the author. Gerrit doesn't re-write the author or committer fields when you upload, and git-cl-upload works locally so it uses whatever you have configured locally.

Even though the web UI will always display a single email address (whichever one you have configured as your Primary in your gerrit settings), your commits will retain whatever commiter and author fields were set locally.

So just make sure that you have the right thing configured in each individual repo on your machine (or use git's fancy new per-directory config: https://github.com/blog/2360-git-2-13-has-been-released) and then it should work as you expect.

I double-checked now and my observation about the "preferred account" are valid.
I have user.email set to kjellander@webrtc.org in my WebRTC repo, and kjellander@chromium.org set in my global Git config.
When uploading a CL, chromium.org is set as the author: https://chromium-review.googlesource.com/518009
Even after changing user.email in the glocal config, I get the same result:
https://chromium-review.googlesource.com/518109

Then, after changing the preferred e-mail in https://chromium-review.googlesource.com/settings/ and re-uploading (wiping previous reference using git cl issue 0 between each test), the webrtc.org account is set as author:
https://chromium-review.googlesource.com/518183

This is quite a blocker for us, and also a source of confusion for users that are mixing chromium.org/google.com addresses in their work.

I'm sorry I missed your 4th paragraph about the Web UI always displaying the Primary e-mail. That explains some of the confusion.

I believe we can close this now, but it's going to be painful to explain how this works for our team members, since it's very confusing that you see one thing and another thing is being committed.

Is there no way to make the "real author" more visible in the Gerrit UI? It seems the information is there somewhere, right?

I guess the answer to #3 is to just check the commit message?

Yes, the commit message (which is part of the reviewable diff) always shows the true Author and Committer fields.