I agree. I bet you will find that the formula for the safe harbor match includes a term for compensation that is defined in the document as being for the plan year.
As for the document provider, I don't think they understood your question. Our VS document (ASC) lets you set the computation period for the SH match, but makes it clear that it can be deposited more frequently during the year at the discretion of the employer. Their answer sounds like they thought you were asking about deposit timing. At least, I hope the IRS didn't approve a document that allows employer discretion to change the SH match allocation formula at any point during the year.