He testified they were consistent with being bullet holes but he could not determine directionality. He must have presumed they were bullet holes however because in his testimony regarding the May 1964 reconstruction, he offered no resistance to being asked if all the holes in the clothes of both men reasonably aligned.
At the time of his post May 24, 1964 testimony, he was assuming that they were bullet holes. And rightly so. The questions that he was being asked in the testimony about trajectory alignment seemed rather pointless after he pointed out to Specter that he hadn't made a very thorough study of the Zapruder film.