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Viewing post in How to make your GameMaker game be TRUE 64x64
Draw GUI will still draw things scaled to real-size pixels even when using this trick. It doesn't care about application surface size or view size etc. That's just how Draw GUI works, and I have no idea if that can be changed or not.
Instead, when you want to draw your HUD and so on, use the normal Draw event, and place stuff in relation to view_xview and view_yview. This'll will give the same result, but use the same scaling as the rest of your game.
Resizing the GUI works differently than resizing surfaces in GM, for whatever reason. The difference is that, as you describe, even after resizing it will still display subpixels (e.g. when you draw a rotated sprite, a primitive such as a circle, x/y positions that are fractions of pixels, etc.). To absolutely force the GUI to adhere to the pixel grid, you could instead draw all of your GUI stuff to a surface that's the desired size, then draw that surface on the GUI layer.