standalone - Can I specify the font size in the document?

standalone uses article as its 'base' class, but you can change this with the class=<classname> option. Hence, you could tell standalone to use a KOMA class with

\documentclass[class=scrreprt]{standalone}

You can then use the \KOMAoptions directly in your standalone files, place it in the font-config file, or add the fontsize declaration to the class options directly.