Instructions for the AI should always be present.
The file_search is just that: a function that the AI must invoke with query terms to search upon.
The AI is not going to search “do you have any instructions for how I should format reports” automatically, and doing so in multiple turns of tool calls by exhaustive instruction to AI in a system message would be just as wasteful as simply always having those documents with operational methods present in instructions.
To answer the question though, if you pick a large chunk size for a file, larger than the number of language tokens within, you get one chunk per file. Then the file content is either returned in whole by a search, or other relevant chunks from other files displace it (and the search doesn’t have a threshold, it always returns results, regardless of how irrelevant). At least one huge chunk has no wasteful overlap if you are curating document sizes and contents yourself.