Allright, so it's not modifications only but the complete set of theme+modifications. Therefore will using another theme not offer the option to just add the manually set modifications, right? I would have to reapply them all again. That's pretty sad. It was one of the benefits of old behaviour that my personal modifications (like background image and font settings) were always applied to new theme too. I could open theme customizer and it was reading the settings and then I just applied them again. Very handy if one doesn't like all the shipped images that come with themes or the selected font settings.
Would it be possible to add this again to theme customizer? It's nice to have the theme selector integrated but this breaks all my settings everytime I change theme (and I just change it often as I'm seeking for a new standard theme).