Hi Noel,
thank you vermy much for you help!
to 1: This is not really the option for me, since I must load my css from the framework page layout and the corresponding UR/HTML files are loaded later from page builder
to 2: This is very interesting! 
I've tried it out and set this session attribute at earliest point as possible (doOnNodeReady in the component, which handles each navigation request in my framework), but it makes the problem even worse: the files are still loaded but now *all* CSS files are loaded from sap_standard path incl. .../com.sap.portal.theming.webdav.themeswebdavlistener/Portal/prtl_std/sap_standard/nn7.css
Have you tried it with UI Theme Designer as well or only with old theme editor?
to 3: This workaround I would avoid, since it results in unnecessary page load and is not good for the performance. But you are right, at the end it can be a solution for the problem
Best regards,
Artem