Thanks for the feedback and advice guys! This was my first go with Edge Kote and think it did a decent job of at least imparting some consistency in the color for the edges.
I do have a set of punches that I can next time, they are "pin punches" but likely will work for this. I didn't use them on this project because I was lazy - they were buried in the garage. But I've dug them out now and should be able to just use a couple of 2x4s to support the leather but not the impending hole. I was also a little worried about whether the punches would tear the leather or somehow mar it - but in reality using the standard drill bits really did that more than a punch will (I think).
The dye job is another "opportunity for improvement" next time - it definitely would have been better to dye all of it before stitching on the reinforcement panel - but that's assuming I would have thought that far in advance.
This has (and continues to be) a learning experience!