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Unfortunately I don't understand what you want to do.
You say you want to modify identifiers with a template. By themselves, templates can't modify metadata. They need to be invoked by something that can change the metadata, such as action chains or search & replace.
You say that selection modifiers (in action chains) are a problem. You can avoid these by doing searches in your templates. One way to do this is to use a chain variable action to compute the identifiers you want for each book (using from_selection) and store the result in a book_var. Then use a template in single field edit to fetch and return the book var, returning the existing identifiers if the book var isn't set. As far as I can tell you would need to select the books with the identifier you want to change. The action chain wouldn't need to alter that selection.
Of course you might be asking a different question...
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