Hi Maximilian
Is there some reason why you haven't used the standard tool UI Theme Designer for your corporate theming?
The UI Theme Designer is the correct and standard provided tool for applying corporate theming to ensure coherence across all apps - both custom apps and standard apps - available for all unified rendering apps - so it covers you for Fiori and Web Dynpro ABAP and other scenarios as well.
I agree with Leonardo - app specific theming is dangerous as it breaks the principle of coherence. Lack of coherence degrades user productivity.
By the way, you should always permit users to choose High Contrast Black theme in addition to your corporate theming. This is also for productivity reasons and to ensure you are providing a UX that works for as many people as possible - e.g. to cope with issues such as colour blindness (8% of males) and low vision (e.g. ageing workforce, shift workers, late night work etc.).
Rgds,
Jocelyn