Hi Maurice,
I have not much experience with setting category themes but my guess why it doesn't apply to programs would be that programs may consist of different courses from other categories.
One way would of course be to use user themes. But then you would need to find a way to assign it.
What we did in a theme for one of our customers is to add a class to the <body> tag depending on the organisation of the current user. From there on you can apply organisation specific CSS rules.
Regards,
Tobias