Some styles are duplicated in VisualStudio2013 theme. For example:

For example, RadButtonStyle is located in:
-Telerik.Windows.Controls.Data.xaml
-Telerik.Windows.Controls.Navigation.xaml
-Telerik.Windows.Controls.Input.xaml

This creates conflicts when I try to change default style of a RadButton because other styles are applied instead.

Reason for declination: 
We understand that having duplicate styles can be annoying for our customers. However in Silverlight the base style in a resource dictionary cannot be omitted. As for WPF, it is possible but will lead to exceptions if there is a missing resource dictionary or wrong order of the merged dictionaries which would be unwanted change for our customers. 

That is why we suggest our customers to merge their custom styles after Telerik default ones thus maintaining and upgrading is easier. Another option (in WPF) is using a custom build of our themes where all unwanted duplicates are removed. If you choose the second, you will need to remove button's style from all XAML files except the Telerik.Windows.Controls.xaml one and edit it there.