I've run into what I think is the same issue, but I've sussed how to get around it:
If I'm in windowed mode and maximise or even enlarge the window a bit, the screen becomes very zoomed in, as if in a grab animation with zoom on, which makes it quite hard to see what's coming at ya (happened to me in the lower city on a self-imposed hard-mode run). If it's minimised and in a smaller window, it looks ok. If I enter fullscreen mode [alt + enter] then it goes back to normal again. I'm using 2560 x 1440, so 16:9 ratio. Changing the screen's scale doesn't seem to have any affect. I do have two monitors as well.
I redownloaded, deleted the save and config files, basically started from scratch. Possibly just a unity issue? I know it can be finickety.
Love the game btw! I've posted the three different scenarios below from a clean download and save as well as the config screen
Minimised (looks good)
Minimised but enlarged/maximised (zooms in for some reason)
Fullscreen (looks good)
The config screen
