I'm waiting. Sorry to be a pain.
I'm not an expert in ancient stone-working in Mesoamerica, but of course it was indigenous Indians. The ancient Peruvians were the people who constructed and inhabited the site, so who else would it have been? Logic guides the answer.
I am more acquainted with stone working in the ancient Near East, where ancient craftsmen used any number of different stone-type drills. In ancient Egypt, for example, diorite drill bits were used to produce the coffers of granite and quartzite sarcophagi. These were hand-turned drills, so the going was slow but it worked fine. And before anyone displays chronic astonishment and declares this couldn't have been done, bear in mind there are many examples of such drill bits recovered in archaeological digs, and many ancient sarcophagi still bear the tool marks of this drilling process. Khufu's is an example, in the Great Pyramid.
I would imagine it was similar at this site. It's Puma Punku, correct? The guy who makes these videos for the hiddenincatours website likes to proclaim that all of these stones are diorite and too hard for ancient man to have worked, but he's decidedly incorrect on both counts. First, ancient man did very well with diorite, and second (if not more important), the vast majority of the hewn blocks at Puma Punku are sandstone, not diorite. Ancient man made plentiful use of sandstone because it's very easy to work.
Why shouldn't the drill hole be straight all the way through? Was ancient man too simple-minded to drill and cut straight? I think not. Drilling and cutting straight hardly requires modern science.
As for the grooves, others have questioned whether they had anything to do with the drilling process, at all. I second that cautionary note. We can't know for sure, and the credibility of the guy in the video is far from solid, so we need to be careful. I personally believe it's possible that something was set into this hole and removed, over and over and over through the years. Whatever the object was that once fit into the hole, it likely scarred the interior of the sandstone bore.