In the module the app/code/core/Mage/ConfigurableSwatches/Helper/Productlist.php is the helper which determines which _swatchAttributeId should be used.
You could extend this module and rewrite the helper.
Rewrite the getSwatchAttributeId function and do you own magic.
You could
just add some id logic, Mage::registry('current_category')->getCategoryId()
add a custom option for a category which you can set per category
read it from the attributeset used for the first product
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