The themes can be easily overridden indeed. Here [0] is example of custom theme applied. For sure the project would really benefit from some pro designer help.
The XAML in Avalonia is great. There is even support for XAML to IL compilation during build so you don't have any parsing overhead when running your app.
The support is great, you can see this example [1] of using custom rendering in Canvas being part of UI layout [2]. You can also see Avalonia in action here [3].