A while ago, when playing around with the in-game CGs, I discovered that they don't actually have to be 00x600 - they could be something like 640x480. However, since the actual game window is 00x600, the 640x480 didn't fill the whole window. Nonetheless, it handled the image without hiccup even though it didn't match the engine's 00x600 resolution.
Seeing how it handled different resolution images so flawlessly, this gave me the idea that 00x600 isn't an actual limit to the game engine, and therefore there may even be some way to change the window's rendered size. However, I don't actually know if this is true, so I figured maybe someone here would have a clue.
One thing I DO know is that the KiriKiri engine definitely can support different resolutions, as shown by "Tenshin Ranman - Lucky or Unlucky!?". However, I do not know if this is possible with Fsn's KiriKiri engine, seeing that Fate/stay night is 5 years older.
It's alright, we feel your pain. Noone wants to admit being gar for Berserker.