If the map is a normal window, this should be possible. However, depending on the behavior of ETS2 when it loses focus, you may notice sound dropout(if the game mutes sound on focus loss), or the picture freezing(if the game pauses/stops drawing on focus loss). In VR this behavior may be different still.
If you set the "Send command to this target" option of your command to your map window, any keypresses you send should apply to that.
For the scrollwheel, you may need to move the mouse cursor over the window before the scrolling will be registered.