Everyone does their doping differently. Remember that at 1000 yards with a decent wind you will be aiming 35+' high and 5' to the side. To attempt to reliably/accurately do this with anything other than adjusting your dope on the scope is IMHO not going to cut it...... depending our your purpose. I spent the weekend shooting the new 1000 yard 8" plate at Best of the West. At a distance where a single 1/10 mil click is enough to miss, I would not condone use of the 100 yard increment BCD or hold over. I do however enjoy hitting the target.
"Are scopes really that reliable now that if they were clicked up to 800 yards or more from a 200 yard zero, clicking back down to 200 would return to a perfect 200 yard zero"
Yes absolutely.... assuming you have a decent scope. I have shot 1k+ rounds with my current Vortex Viper PST 6-24 FFP. I fine tuned my 250, 500, 750, 1000 numbers for my ammo. At BOTW, I can sit in one position and shoot all these distances. I change target distance all the time during shooting. I have never fired a round that was more than the influence of the wind off. This holds true trip after trip after trip. If you doubt your scope, shoot a +5-North-South-East-West and see how it does.
"shimmed the rear scope mount"
With most standard scopes and most standard rounds, you will probably need to add a 20MOA base in order to totally dial out the elevation at 1000 yards. I recommend purchasing an angled base specifically designed for this.
"I just marked an alignment dot on the edge"
On most modern long range target scopes (like the one I mentioned above), the line is there and the cap is removable so that you do not need to do this.