It turns out that Gnome differs from other Linux window managers in that it makes Java aware of the system antialiasing settings. As a result, Java picks this up automatically and behaves as it does on Windows, which is to say, the application obeys the system setting.
However, other Linux window managers do not supply Java with the antialiasing, which is why the checkbox exists, so that you can manually turn on antialiasing.
So on Gnome, the behavior is as follows:
Gnome setting MATLAB setting MATLAB result ------------------------------------------------------------ Monochrome (No AA) No AA No AA Monochrome (No AA) AA AA LCD AA No AA AA LCD AA AA AA
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