Firstly, read the FAQ What is the difference between different kinds of hot keys? to understand the difference between menu command keys and hot keys.
Applications sometimes let you adjust their menu command keys, and otherwise you can often adjust them in the System Preferences Keyboard, Shortcuts, App Shortcuts preferences.
Applications usually do not have hot keys (unless they have some facility to work when the application is not at the front), but if they do they will generally have definitions for them in their preferences.
Applications also have various other keys that may mean things when using the application, such as for selecting tracks, or changing tools or whatever, and they are generally specific to what you are doing in the application at the time.
If neither the application, nor the System Preferences allows you to adjust the keys, then the only remaining option is to have Keyboard Maestro use a hot key and then simulate the desired keystroke. The problem with this is you can only safely map keys in one direction (so you can make X mean Y, but not then make Y mean something else), and also that it is often hard for Keyboard Maestro to know the context sufficiently to know when to do the mapping (for example, if X means Y, you can no longer type "max" in a text field).
So the answer is very much “maybe”.