Go to your display settings and scroll down to "Scale and layout" and set it to 100%. It will make all your icons small on your desktop but the game wont be zoomed in anymore. Just set it back to 125% once you're done playing.
I am not an expert but I had a somewhat similar problem with one old VN, only it didn't want to go fullscreen and was always stuck in native (super small) resolution. Fiddling around with video cars options solved the problem.
You can disable scaling for a single app only on windows, then you won't need to change the system settings every time you play it (right-click on the executable -> properties -> compatibility -> Disable display scaling on high DPI settings)
