Would it be possible to have more precise control over the menu button location instead of just Top/Bottom/Left/Right? With the mods I have pretty much all those options it ends up overlapping over something, and when I do find a good place for it and go from the VAB to In-game or vice versa, some UI elements move while MechJeb stays the same so it will be clear of icons on one screen but not the other

You can drag the menu button with the right mouse button.