Do barrel harmonics come into play due to the charge variation?
I believe harmonics play a role but there are other factors as well. Powder burns differently at different pressures and the pressure obtained with identical cartridges in different guns can be quite different. If the powder burn is inconsistent, accuracy will suffer. Also, bullet rpm will change with different velocities and can affect bullet stability. Then there is the barrel twist rate; if the twist in the barrel the load was worked up in is different than the barrel you're shooting, accuracy could be affected.
I know the charge accuracy between rounds is important, and also the depth the bullet is seated. I believe bench rest guys want the rifling to barely touch the bullet.
Seating the bullet to almost touch the rifling compensates for things like inconsistent neck tension, a suboptimally aligned throat, etc. If the barrel, throat and chamber are perfectly aligned and the neck tension is consistent, having the bullet almost touch the rifling is less important. In the case of Barnes bullets, and I presume other copper bullets, you will probably get better accuracy with the bullet not almost touching the rifling.
I am not looking for one hole groups, just good consistency between various off the shelf loads. Perhaps this doesn't exist.
Yes, I think you're asking too much. Even with good handloads, it would be the exceptional gun that didn't have a decided preference for a certain bullet/powder charge combination. Factory loads have to be a compromise between all the guns they will potentially be shot in. Just be glad if you can find at least one factory load that works well.
50 yds for the contender is not asking for too much...am i? 
In a scoped Contender handgun with good handloads and reasonable cartridge selection, I would expect to get no worse than 1 to 1.5 inch 3 shot groups at 100 yards and some will do quite a bit better. Some cartridges aren't designed for 100 yard shooting and won't do as well (for instance such things as 9mm Luger, 380 Auto, etc.). I've never worked with a scoped 357 Magnum so don't know how it would do at 100 yards; I suspect it would do fine and there should be no problem with 50 yards.
