Okay, I was able to reproduce the problem by setting the DPI scaling on my system to 150%, and trying to run the game in a window at 1600 x 900 (while monitor resolution was set to 1920 x 1080). This failed and opened a smaller window of 720 x 480 (or something). However, after I modified the manifest on the .exe file, as described in your link, it now works, and does not try to scale the screen up.
Here is the link on how to update the manifest: (placed here for anyone else so they don't have to read through all the posts)https://docs.microsoft.com/en-us/windows/win32/learnwin32/dpi-and-device-independent-pixels
Now, here is a link to a program that allows you to edit the manifest:http://www.restuner.com/download.htm
There are other ways to do this, but this seemed like the easiest. It is not a free program, but has a 30 day trial. I will probably buy it once that trial is up, since I plan to keep doing this in other projects...
To edit the manifest, first install Resource Tuner, and click yes for the context menu shortcut. Then right click on your game's executable file, and select "Open with Resource Tuner"
You will see three folders, "Icon," "Icon Group" and "Manifest." Open the Manifest folder, and double click the manifest file.
Here is what I used in my manifest.
<assembly xmlns="urn:schemas-microsoft-com:asm.v1" manifestVersion="1.0" xmlns:asmv3="urn:schemas-microsoft-com:asm.v3" >
<ms_asmv2:requestedExecutionLevel level="asInvoker" uiAccess="false">
This combines the existing manifest with the additional stuff provided by the first link to Microsoft above...
For me, it now runs the game correctly, regardless of any DPI scaling. The game is not actually DPI Aware - it does not increase the size of the text or anything - but it will not think the screen is the wrong size as it was doing before.