The backbone will not be informed of your change of URL if you do it manually. This change will be captured by the browser, and it will do its job by sending a request to the server, as usual.
The same, if you click on a regular link, it will follow its href without specifying a baseline.
If you want Backbone to be responsible for changing the URL, you need to do this using the basic tools available to you, and this is your own router.
So, if you want to change the URL in Backbone mode, you need to do it explicitly, for example:
app.router.navigate("my/route", {trigger: true});
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