Hi Jack,
Thanks for your patience.
We have checked your query “How do you apply different custom themes or built in themes in a MVVM app at run time” and we would like to let you know that we can apply the custom themes or built themes by using Theme property of SFSkinManager. Please refer the below sample for the same.
In this sample we have used custom theme (Theme Name:CloozLight) for FluentLight.
Please try it with the above solution and let us know if you need any further assistance on this.
Regards,
Elakkiya