Very likely, but try this steam list for low-end FO4 gaming, which itself uses 800x600. There's always a minimum resolution, not just in Fallout 4 but any game - and in all other software and operating systems. It's not just out of wanting it to look a certain minimal "niceness" but because there will be some things that'll have a minimum pixel count to function or display actions properly on screen (say, turning a lock through degrees) or being able to list on-screen menus & maps, or differentiate between different stats, etc.
I agree it's a bit pixeled especially with text. GameCompanion always works great for me in Windows 7 for stretching up the window, but unfortunately is really pixelated in Windows 8, 8.1 and 10 for some reason. Maybe this mod is having the same problem?
If I start the game via Vortex nothing gets upscaled. The game is just in the resolution I set it to. If I launch the game via the normal launcher it instantly crashes to desktop.
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Crash log - https://pastebin.com/qRajCDeN
Installation: