Apparently, I have to switch my control between Internal and S/PDIF which is unfortunate every time I turn on or off my Kemper.
Yes, that is true, that's a thing you need to do every time if you want the Kemper to be the source. Some KPA's can also slave to an outside clock, for example your Focusrite interface. I don't know the details, but some early KPA toasters don't like this so much. Have you also connected the Focusrite S/PDIF output to the Kemper input?