This is on Windows 10 with Desktop scaling set to 150%-- there are 2 monitors attached(a 4k and a 1080p)
If I boot up the game in borderless windowed mode it stretches it across both monitors, and some of it is offscreen. The game uses D3D11 for rendering.
By adding a call to SetProcessDPIAware prior to creating the window, the problem was fixed.
Anyway it appears that SDL_WINDOW_ALLOW_HIGHDPI is not doing the correct thing, or not doing anything.