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I am not aware of any chance to give a list of selected filepathes to the commandline of an external application directed by the tool feature of Mp3tag.
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If tool option "for all selected files" is checked, then running the application against each file is expected behaviour.
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What is the maximal size of the commandline in your environment?
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You should study the call syntax of your application.
How many parameters can your application accept on the commandline?
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Does the application allow to collect filepathes into it's own file queue?
(Like WinAmp /ADD "%_PATH%" will do.)
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Does the application can work with a textfile containing multiple filepath entries?
If so, then Mp3tag can export a textfile containing filepathes, which can be used further on used by your application
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What application is it?
DD.20100925.0637.CEST