I have a Remington 7400 30-06 with a leupold vari x-ii variable and leupold base/rings. I have been using the 165 gr AccuTip for a long time and since they are getting almost impossible to find I tried some Federal ammo (180gr) that I picked up cheap when a gun store was going out of business. We stop at a range on our way to the hunting cabin most years and check our bzo @ 50 yards. It was dead on with the Remington ammo. I wanted to see if the federal would shoot in the same hole. It did not. I don't remember exactly but It was probably ~ 2" off in elevation (low) and windage. Still not quite as extreme as your results but some weapons have a favorite load. The box test can tell you if the scope is ok but if you and or rifle can't shoot decent groups I'm not sure if it will tell you much.
Your last is what I was worried about with my Sako as I’ve only been shooting about 3 1/2 years. But my AR-15 I built I was getting Sub-MOA groups with match ammo repeatably. But I still worried I was flinching or something. Nope. Not me, scope (glad it wasn’t the rifle. It’s a hand-me-down frommy wife’s uncle and it is a beauty!)