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.
If tool option "for all selected files" is checked, then running the application against each file is expected behaviour.
What is the maximal size of the commandline in your environment?
You should study the call syntax of your application.
How many parameters can your application accept on the commandline?
Does the application allow to collect filepathes into it's own file queue?
(Like WinAmp /ADD "%_PATH%" will do.)
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