Any changes made in Style Propertes will update the corresponding class in the templates.
In the case of the sign up button for example, the content between the
@property "signupButton" and
@property "/signupButton" tags will be updated.
This is how the system has been designed - so changes can be made in Style Properties or the templates.
See this section of the Help Manual:
http://xenforo.com/help/css-templates/