Sexan,
Not exactly, this JS_WindowMessage_Intercept intercepts commands in window. This does not affect on JS_Mouse_GetState. You can simply disable WM_LBUTTONDOWN when the mouse pointer is over the required part of the item(Before pressing button). Instead of switching the modifier on the fly. And in another zone, enable WM_LBUTTONDOWN.
Use this command to disable
reaper.JS_WindowMessage_Intercept(arrangewindow, "WM_LBUTTONDOWN", false)
And this to enable
reaper.JS_WindowMessage_PassThrough(arrangewindow, "WM_LBUTTONDOWN", false)
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