You probably can't without messing up the desktop. Window manager shortcuts are global, so if you change them, it changes for the entire desktop.
Another thing to consider is that there are other keyboard layouts too (not everybody uses a USA keyboard), and not all keyboards provide the same set of keys. Maybe a keyboard doesn't even have LEFT ALT.
I believe in a system that is inherently multi-tasking, it is extremely bad behavior to assume you are the only program in the world, or to assume you can decide for the user how he should use the computer. I am very allergic to programs that take away my controls. If a program does not work cooperatively with other programs (cannot run in windowed mode, locks the mouse cursor in the application, or changes things I am used to have (like global key shortcuts etc)), that program dies a very ugly death really fast.
Some of that allergy is born out of experience, programs locking me in and then crashing, leaving the keyboard in an unusable state, with a system where I have a dozen other applications running that I want to close down nicely. I haved used multiple desktops for the last 20 years, I never run one application exclusively.