...indesign behaves differently to quark (quark not a problem), which means you need to work differently in the end with global overprinting spot colors...
...generally speaking spot colors in most instances need to be knocked out unless in very special circumstances and in those very special circumstances you can advise your print provider to ensure a spot color does overprint when ripped, even though the source artwork isn't overprinting, the data still exists behind the spot color for a reverse situation to be made in a commercial RIP...
...the other option is to use acrobat pro with third party software like Enfocus Pitstop or Arts PDF Crackerjack...
...normally for users of indesign the global overprint issue is not a problem as they can inform the print provider of their needs if a global overprint is required on supplied artwork on a given spot color and any reputable provider will have the tools to help...
...in most cases, for things like varnishes, they are created on different layers by designers and this kind of work is normally pre-meditated, so layers can simply be turned off or the work has to be created with overprints "manually" inside indesign as you go along...
...if you are dealing with someone else's file and you don't have the tools to fix it, then you have the choice of charging them to fix it, or get them to do it if the exported spot color really must be overprinting everywhere...
...and lastly, as mentioned, informing your print provider of your requirements...
andrew
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