Rotate the ATLAS to match the view in the finder. That's what we all do. With a Newt finder on a Newt main scope all three will then be the same orientation no matter where you have the scope pointed..
Mental exercise: Your dob is pointed halfway up the sky and due east. The focuser on your dob is set up to be 30º above the horizontal for easy viewing and is on the right side of the tube (from behind). You are sitting upright on your stool. Q: Where is North in the eyepiece view? Repeat for a bunch of other parts of the sky. (Bonus points for viewing just below Polaris!). North and the direction of drift can be just about anywhere in your seated view through the eyepiece...
My point is that we all rotate our atlases already to match the sky in whatever direction our dob is pointing. I just think that once you get the atlas/finder the same orientation it is nice to not have to do a 180º rotation to get the view in the main scope to match the first two..
We don't all rotate our atlas's. I am not using a paper atlas, I am using Sky Safari, my sky view is permanently aligned to the alt-az axes. I am not using north-south, east-west. When I move the scope on in the azimuth direction, the view in the finder moves in the azimuth direction, oriented by the cross hairs.
SkySafari has many capabilities that a paper chart does not have. When I am using the magnifying finder, I choose a view that is appropriate for a 10x50 finder with cross hairs and a 6.4 degree TFoV, the cross hairs, the finder field, the star magnitudes are all chosen to match what I see in the finder. Since Sky Safari is providing me with the cross hairs, it's relatively straightforward to simply match the view in the finder to the Sky Safari view.
I can use stars anywhere in the field to align the finder cross hairs so putting objects in a small field of view of the main eyepiece is very doable. With the 22 inch, hunting down galaxies, I will often use the 10mm Ethos as the finder eyepiece. That's about 1/3 of a degree at 280X. This is simulation I made of finder view on the way to centering the target.
With a paper chart, you only have the one chart magnification so maybe aligning them makes sense. But when I move from the finder to the main eyepiece, I zoom in so that now I am looking at a star field that matches what I see in the main eyepiece. I can adjust the magnitudes of the stars and galaxies/DSOs to match the what I am seeing.
This is very different than using a paper atlas, I don't really see any advantage having the finder view and the main scope view aligned in rotation because they are so very different. When I am working in the main eyepiece, I am looking at a chart that is appropriate for the main eyepiece. It's relatively easy mentally rotate the image because the two are well matched.
And as I asked, how are you mounting and aligning your Newtonian finder? Is this something you use every time you observe? Have you tried an electronic chart like SkySafari? I switched over from paper to electronic charts more than 20 years ago..