The problem is, MMF2 doesn't let me change between a blurred or pixely upscale at runtime either. I can only make that selection at edit-time, so, I'd need yet another executable.
You can have both blurry (with black borders) and pixely scaling at runtime with MMF2. My Knytt Stories mod does it. No, it's not a simple or obvious solution, but it works like any user would expect it to.
Your base frame is a black box that does little more than use the Sub-Application object to launch the game's starting frame. Also, make sure to add the Window Control object to the black frame and every game frame. The parent frame has the menus, so the child frame is unaware of menu commands. To communicate between the windows you'll need to share something between the parent and child. I used "score" because "Global values & strings" didn't work for reasons I can't remember. These options are found in the Sub-Application object. Add the communication logic to the black box frame and every game frame. Here are the messages I used:
Player Score is used to communicate with the child window
0 = 100% zoom
1 = Child requests exit fullscreen, occurrs in Install frame
2 = 200% zoom
3 = Parent requests child to un-zoom for fullscreen
Set the program to "Resize display to fill window size." Add menu logic to the "Global Events" area. The most important thing to do here is when fullscreen is enabled change the window size to clientheight and clientwidth. When reverting to windowed mode set the window back to its normal dimensions. Use the Sub-Application object to properly position the child with all resizings.
In each game frame the frame needs to check to see that it is properly sized on frame load. Each frame also needs to listen for messages so it can change appropriately. The Window Control object is used to change window size and position.
Why this method works: When the user selects fullscreen, the base window is stretched and blurred, the screen resolution is altered, but child window is not stretched. It appears larger and blurred because of the screen resolution change. When switching to a 200% zoom in windowed mode, we get a pixel by pixel scaling because the child window scales by it's own rules. The black borders are simply hidden behind the child window in windowed mode. Yes it's hacky and overly complex, but the user experience is clean and simple.
I hope I haven't left out any important bits. I figured this out middle of last year, so I'm fuzzy on the details, but I'd be happy to make my KS mod's source available to anyone who asks.
Just to be clear Nifflas, I'm posting this as I think it may be a useful technique to use in your future Multimedia Fusion based creations.