So, that person's flags will get reviewed. (That's part and parcel of YouTube's heroes). YouTube will see the pattern of that person just flagging people based on disagreement with content. His flags will get rejected, he will not get any points, he will not level up.
In contrast, anyone could easily flag his comment. That flag would also be reviewed. YouTube will see that that flag is addressing a legitimate instance of harassment (not simply disagreement with content). That flag will be sustained, that user will have a community guidelines strike, and the person who flagged his comment will get a point in the YouTube Heroes system.