Here's a quick way to get your flint to line up parallel to the frizzen. Easiest way I've found to do this is to simply hold the firearm in your lap, right side up.
Mount the flint in the jaws using just enough tension to hold it in place, but will still move fairly easily. Ensure that the back of the flint is seated in the leather and against the back of the ####.
Bevel up or down...makes no difference. Bring the firearm to full ####. Drop the frizzen down as it would be in firing position. Now....this is the tricky part, as it seems like you might need an extra hand...holding the #### firmly in one hand, while holding the frizzen in place with the other...pull the trigger and slowly lower the #### until the flint rests lightly, but firmly on the face of the frizzen. Checking of course, that the inside edge of the flint is not contacting the barrel. At that point, its edge should be perfectly parallel to the frizzen's face. Ease the #### back enough so it clears the frizzen, then snug the screw holding the flint down so that the flint is held securely. But not fully tightened down. Check the alignment again, by repeating step one. If the flint is still parallel, tighten up the screw fully. Recheck. If still good, you are done. That should give you a perfectly square flint, every time. Takes a bit of practise, but once mastered is quick and easy. In the photo, your #### and frizzen do appear to be out of line. It is also possible that the flint is too large. Do you have an instruction manual for the rifle? If so, it should give the right sized flint. Otherwise, the Pedersoli site should have the information you need. Hope this helps.