From my understanding, you want to change the Keyboard shortcuts preferences for different actions of the command window.
You can change these in the Preference Panel. Go to ‘Preferences’ under the ‘Home’ tab in the toolstrip. Navigate to ‘Keyboard -> Shortcuts’ from the left panel of Preferences.To modify shortcuts for scrolling through code history, search for action name: ‘Previous History Command’ and ‘Next History Command’. You can just click on the shortcuts specified and enter the new shortcut (using the corresponding key from the keyboard) that you want.
To modify the shortcut for scrolling in the command window search for action names: ‘Page Up’ and ‘Page Down’. The default option specified under ‘Tools with shortcut’ will be ‘All Tools’, this can be changed by clicking on it and selecting only ‘MATLAB Editor’. Create a new entry using the ‘+’ symbol with the new shortcut value and the ‘Tools with shortcut’ as ‘Command Window’. This step ensures that the shortcuts are modified only for the Command Window and not for all the other tools.
Click on Apply and OK to save the new preferences.