Separate page-title and header-title for index page.

You are experiencing what is called hybrid or combined approach to application design, where html templates rendered by server are duplicated and expanded in the client with JavaScript. This makes Misago appear to run very fast and makes it harder to notice the delay before JavaScript loads for first time, but also makes it confusing to customize looks. The issue you are bringing here comes up all the time:

misago-project.org/t/category-customization/358/
misago-project.org/t/how-to-change-the-thread-template/396/
misago-project.org/t/category-customization/358/
misago-project.org/t/customizing-misago/520/
misago-project.org/t/how-to-custom-the-thread-page/573/
misago-project.org/t/add-title-to-categories-redis-and-updating/456/

...and after having dealt with it for two years, I can say that it was bad idea to have static HTML fallback for React.js application, as it turned out not only annoyingly time consuming to implement changes to the theme, it is also confusing to people trying to customize theme further

Would it be possible to separate these two things?

Not really. React.js component needs to takeover anything between navbar and footer to work as we are also updating the header when user navigates to other category.

Short term solution would be adding new setting to "general" settings, but adding settings for customizing how things look to the admin panel is something I'm weary of. I've used to have bunch of settings controlling how things were displayed in my first forum software, and that was nightmare to maintain.

In long run I would like to have a way for people to customize Misago easily via "page builder" in our admin panel, but thats years away.