I havent tried this but maybe we can set it to none for transparent?
From: http://jquerymobile.com/demos/1.2.0/d...
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theme string
default: null
Sets the color scheme (swatch) for the popup contents. Unless explicitly set to 'none', the theme for the popup will be assigned the first time the popup is shown by inheriting the page theme or, failing that, by the hard-coded value 'c'. If you set it to 'none', the popup will not have any theme at all, and will be transparent.
$( ".selector" ).popup({ theme: "a" });
This option is also exposed as a data attribute: data-theme="a"