I think there are two different issues here:
* In a civil war, one side retains the original tag of the country and is the 'true' version of the country and the other side gets a dynamic tag. The dynamic tag gets the generic focus tree unless the content designer adds provision for them to have a custom tree. I think this is quite fiddly, so it's rarely done except for very prominent civil wars like Spain. It usually doesn't matter, since the dynamic country is generally just a speed bump for the 'true' country. I believe that the specific (Reichskommissariat?) focus tree you have posted is from a mod. I don't recognise it; I can't find loc entries for the focus names; and I don't believe Paradox would make a focus called "Black Sun Rising" with a swastika icon. So I think it is an error with some mod you have running that gives them that tree rather than the generic tree. As for getting the generic tree over the country's proper tree, if it's a problem then it's a design problem, not a bug.
* When a country gets puppetted, if there is nothing to tell it to switch paths, it will not switch paths. You can hopefully appreciate that it is quite time-consuming for a content designer to anticipate various different scenarios like this and decide exactly which focuses should be wiped clean and which should be completed. These focus trees are primarily designed to be played, not for scenarios like this. I agree this is a problem, especially if there's ticking support for the old ideology in some spirit, but again, it's a design problem, not a bug. You'd be better posting in the main forum or the suggestions forum if you feel strongly about it.