Is it possible to have a Google Chrome shortcut use a different user agent than an existing Chrome window?

What you can do is create multiple profiles. This means that windows will not be shared, and likewise with favorites, cache, home-screen content, cookies, etc., but you'll be able to make your shortcut work the way you wanted it to.

First, follow the steps in this article here to create a secondary profile for Google Chrome: Create Separate Profiles in Google Chrome for Family Members and Stay Extra Safe.

Secondly, modify the shortcut by tucking on your --user-agent parameter. For instance, here's the command line I used to test:

"path\to\chrome.exe" --user-data-dir="..\User Data\Test" --user-agent="Mozilla/4.0 (compatible; MSIE 8.0; Windows NT 6.0)"

Now you can double-click on your regular Chrome shortcut, and this new shortcut, and each will open their windows in distinct sessions, with their own user agents.