One thing you can do is go to the Model View Options Dialog and modify the Model View Option used in the Views which are published as PDF for further work in PhotoShop/InDesign.
In the Model View Options Dialog go to the "Override Fill Display" panel and check the "Override Fill Background Color" checkbox, then select the "Transparent Background" radio button.
With this MVO setting none of your elements will have any fill backgrounds (they will all be transparent).
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