Sabotloader, I'm brand new to muzzleloading, but not to PBR, which I do with my 30.06, and plan to do with my new Accura Lr-X. All I've done with the Accura is play with ballistic runs from Hornady.com (
Ballistic Calculators - Hornady Manufacturing, Inc) based on reported muzzle velocities from here and elsewhere on the web. I use Jack O'Connor's suggestion of no more than 4" rise above the line of sight" (O'Connor 1978 The Hunter's Shooting Guide. Outdoor Life Books) showing my age here.... so I play with the program by trying different "zero" ranges to get as close to that as possible. That's just the first step. Regardless of what value you use in your trajectory, the point is to get your trajectory as flat as possible with your rifle, with ranges you expect to shoot at, as you point out. Your points are well taken about not messing with the scope but using holdovers. With my .06, I can shoot to 400 yards w/o using any of the ballistic marks, by calculating the % up the body to shoot. By working all this out before hand, I find I'm much quicker and accurate in field (and tested at range before hand of course).
So, I work on the animal's anatomy and determine where I want the bullet to hit (center of vitals of course), and work this with the trajectory in a spreadsheet. Simple concept, but you have to figure height of animal (brisket to top of back @ leg, or trailing edge of leg). Again, Jack O'Connor has these in books, but Chuck Hawkes
North American Animal Anatomy (thanks Chuck Hawkes). So I calculate an exact % of body to aim at based on that particular distance and trajectory, to hit center of vitals. Then I get more realistic and find a hold that works for most of the ranges. With my .06 I usually find a single hold that works well up to Maximum point blank range, then %'s to comes up from brisket for 350, and 400, for elk or oryx. so I have 3 holds in my head while I'm stalking. This way I don't have to guess or otherwise dither when I get the opportunity to shoot. I've already worked it out on paper and at the shooting range. I range rocks and trees as I stalk, never time to range an animal, unless it's pretty far away. If I stop somewhere on trail or saddle, then I range places around me.
I have attached a spreadsheet I've started for a pronghorn hunt so you can see my approach, which is slight extension of what you've already done. I used O'Connor's 4" value as a start. But I have yet to test to find my load and what I'll actually use. That is why you won't see a column next to the estimated trajectories with a "common sense" holds. I need to punch holes in paper at the different ranges to finish this up. However, this approach has worked well for me on elk and oryx center-fire hunts. It's just trajectories and groups I can get at the different distances.
I should also mention that like O'Connor, did, I hunt in the West. I may walk 5 or 6 miles in a day for elk, at least for another year or two I hope. If I new my range was limited to 200 or 300 yards, I wouldn't maximize my point blank range, but I'd maximize the flatness of trajectory for that situation.
In either case, I applaud you for working and thinking about your trajectories and checking them on the range. I think it's an important and ethical thing to do, besides interesting, and it has given me the information and ability to very quickly acquire target and shoot without guessing, or minimizing the error around mistakes in guessing range to be more accurate.
I hope my Accura shoots as flat as your's appears to!