Dwalin,
when extension b has its message lamp set to a's number it means that when there is a message for extension a, the MWI on station b is lit. If there is a message for b, the lamp on station b will not be lit because the lamp is set to light when there is a message for a. Also the lamp of station a will not be lit because the MWI on station a is not set to b's extension.
Bottom line: The fact that b's MWI is set to extension a will not have an effect on a's lamp when there is a message for b.
With regards to your remark on "masking the symptoms" I can say that's correct, indeed you are masking symptoms. But that doesn't mean the problem is solved. It merely gives you time to investigate why the lamp is being lit (using status station and the message waiting field), without the lamp itself being lit all the time, which is, in my opinion, more "end-user-friendly".
Strangly enough this part was missing in my previous post, though I am quite sure I entered it... Glad that you noticed this!