Yes, lots of this will go away after first firing. Necking down induces RO. I get less when I neck down in 3 steps with 3 bushings. You can straighten them pretty easily drill a neck dia hole in your bench, a block of wood or 1/4 piece of aluminum. Drop it in and lightly push where needed. But you want the case supported at the neck, not on the bullet so you don't loosen the neck tension.
I pay less attention to this these days since I started running min spec reamers in the throat area. When the bolt is closed it will be centered.
If your custom rifle is shooting 1 moa at 500 I would relook at load work up.
Just my opinion
Jeff