without going out to look, (im a lazzy ass today and still in bed a 11am :P) wouldnt cutting them flush leave the depth to tap a thread a little shallow? wouldnt want the bolt hanging down interupting outflow.
there again as im type this i supose there has to be enough to allow a interfearance fit so it should be enough for a tap.
might be a slightly neater job but if your going to that much extra effort from either a holeshot kit or a simple tap and bolt then the Ebay kit and spiggot removal might be worth going a little further again as it is prob the neatest finish possable.
i went simple tap and cap head bolt, its hard to see it from most angles and dosent look out of place. if i had to do it again i would go holeshot kit though.