I replaced the default favicon with my own one in the /templates/[my_template] directory, and I got surprised, because the old one hasn’t been replaced.
I didn’t understand, why and I looked at the source code in my web browser and I found this line:
<link href="/plugins/system/jat3/jat3/base-themes/default/images/favicon.ico" rel="shortcut icon" type="image/x-icon" />
So, the favicon available for the base theme in the /plugins directory is used by T3.
Well, I think, it would be better to use the favicon uploaded into the /templates/[my_template] directory, because this is the standard way. and in the case of the plugin update my own favicon will be overwritten.