Thank you for writing.
That is correct, setting the ApplicationThemeName via the ThemeResolutionService will have higher priority over local control theme settings. To achieve your goal, you can use the ApplyThemeToControl tree method for each form in your application and also, set the desired panel's ThemeName:
Off topic, the other thread which you have opened regarding the same matter ("ThemeResolutionService Is Overriding Custom Theme") was deleted due to duplicity. Please avoid posting the same question more than once.
the Telerik team