Exactly. It will crossfire.
I don't think you realize how little that matters.
Lets do the math. Pretend there is a 5 degree angle between the vertical cross-hair and the bore of the barrel. How much does that offset the bore to the left or right? Depends on the height over bore. Lets say that is 2 inches.
Doing the math results in an offset of 0.175".
Diagram is looking from directly behind the scope, cross-hairs level.
Now since we zeroed at 100yds, the axis of the bore and the axis of the scope aren't parallel, they intersect at 100yds.
Diagram is looking from the top.
X equals 0.00278521 degrees.
So at 200yds, the point of impact will be 0.175" to the left of the point of aim. So yes, technically, you will "crossfire". 0.175" @ 200yds equals 0.0836 MOA
At 300 yds, the point of impact will be 0.35" to the left of the point of aim. 0.1114 MOA
At 400 yds, the point of impact will be 0.525" to the left of the point of aim. 0.1253 MOA
At 500 yds, the point of impact will be 0.7" to the left of the point of aim. 0.1337 MOA
......
At 1000yds, the point of impact will be 1.575" to the left of the point of aim. 0.1456 MOA
So much less than 1 click on the 1/4th moa windage turret. Or a fraction over 1 click of a 1/8th moa scope.
Like I said, inconsequential. If you can read the wind to the degree that you can shoot the difference of 1.5" at 1000yds, you shouldn't be down here shooting with us mere mortals.
A simple level over the scope rail and a plumb line for the reticle will get you close enough that you will never notice any error.