Is there an App or Extension that allows for per-window zoom/magnification? As the title says, is there a Mac app (Mountain Lion) that will allow me to specify a fixed zoom/magnification amount for a specific window, in a specific app?

I use a particular application (Reason from Propellerhead Software) that does not support any zoom levels for its windows.  One window in particular has lots and lots of tiny little detailed text and buttons in it (the Rack) that is often just way too hard to read, even on a 21" monitor set to 1024x768 resolution.  

I would like to zoom this one window, and only this window, to maybe 125% or so of its current size.  I can do this with the built-in Accessibility zoom feature, but then of course that "magnifying glass" focus area follows my mouse cursor all over the place.  I would like ONLY that window to be displayed in the zoom area, if possible.

Just to be clear, this is not about maximizing the window to the screen, but magnifying the visible contents of the window (primarily to make fonts larger).
What you ask isn't possible.

There are apps that will zoom a portion of the screen - I use the loupe in Xscope for this purpose and it does a very nice job of magnifying the area around the cursor, but it's not able to grab an entire window and zoom it in place.

The OS takes the content that the application draws and maps that onto the space where the window exists, so you would need to fundamentally alter the screen rendering on OS X to force an app that hadn't considered zoom levels to zoom only itself.

Unless you really like Xscope, my guess is you'll get in the habit of zooming the entire screen or possible find another software package to replace the one that won't zoom.

The other workaround would be to run that program in a virtual machine and force it to be full screen zoomed in that one OS and keep the rest of your programs running outside the VM. That would accomplish exactly what you ask at some level of time commitment to virtualize the OS and get that set up.