If we can identify the original passages from which titles are taken, our policy is to romanize in accordance with the original. Thus, a title should be romanized: "ka-homer be-yad ha-yotser", based on the prayer in the Selihot which begins: Ki hine ka-homer be-yad ha-yotser."  A 246 3- with "ke-homer" would also be helpful, since some people might interpret the title this way.  By doing this we're not "ascribing words in the title that are not on the piece," just offering an alternative reasonable romanization of the consonants on the piece.

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When there's an actual verse that matches a title,  it's best to romanize the title to match the verse.
Thus, the title of a book by Ahron Soloveichik should be "Para.h ma.teh Aharon" based on the text in Numbers 17:23 which reads "para.h ma.teh Aharon".