I don't mine the holes I had to put on the inside of my panels. Mainly because I had some bracket fitting issues and needed the panels off to deal with it. Plus when I started to put the bolts in, a couple of them had a hard time getting the treads started. I wouldn't have been able to get those bolts on with the panel sitting in my way.
Suggestion: There is a plastic "clip" on the inside top of the panel that they tell you to remove. I wasn't sure what they were talking about but once I tried to fit my panels back on with the brackets in place I quickly saw what they were talking about. You have to remove those with a utility knife so that your panels will fit correctly in the door frame.
Also, be sure to measure a few times to get your upper holes correct. On my passenger side I came down a little too close to my speaker grill and once I mounted the bar you could see a bit of the hole exposed from under the bar. I was able to fix it with a plastic plug much like the ones we use in the door frame. But know this, those inside panels cost $295.00 each from Ford.