Template designer will use whichever window is set as the system default (it ignores any view rules that you might have in place). So it is entirely feasible that when clicking your new Incident shortcut, for example, you will see a completely different window design than you will when clicking to create a new Incident template.
The reason for this is that you might want to have one "template window" design with every attribute on it that you may ever want to use. Just prior to designing a new template, with all users out, you can set this as your system default and then when creating the template you know you have the ability to set a pre-defined value for any attribute in that template. You can then set the system default window back as it was via window designer after creating the template. This is easier than having to play around with view rules to be able to do this.