PA do not use real fullscreen, it's just normal borderless window on top of your Windows desktop. You can even see how exactly it's works within SDL2 source code. With appropriate code you can easily show other window on top of it. Though most of programs that do introduce overlays don't take it into account and always try to mess with any applications using D3D / OpenGL. Considering they usually programmed by guys that have very limited understanding of 3D APIs it's end up badly very often.
It would be interesting to known what Raptr does, that kills of mip mapping this badly. My guess would be that it does limit the colour/component formats for render buffers and/or frame buffers in some wonky way, which can cause a lot of trouble when you try to store bit correct information in intermediate frame buffers (like texture coordinated and mipmap levels in gbuffers for deferred rendering, which is what Uber does).
