I am not sure I understand this. The R5ii has more AF points than the R1 and so has more focussing pixels in any particular area. The R5ii sensor will focus with more difficulty when the changing contrast is in the vertical direction (landscape mode) but will focus better than the R1 when the contrast change is in the horizontal direction because all of the R5's detection is in that direction whereas the R1's crosspoints are only 50%. At 45 deg, they should be about the same. Where is the flaw in my reasoning?
From my understanding it's the other way around (but please correct me if I'm wrong).
The R5 should be able to detect phase differences in vertical features better, as the subpixels are aligned in a way that they would see the exact same thing on a horizontal feature.
Think of the old analogue rangefinder style cameras. That's pretty much how dpaf works.
You see two images combined to one from two different angles. If the lens is out of focus, you see two images side by side that are not aligned ghosting around, so you pull focus until these images combined.
Now imagine a black line on a white piece of paper. If the line is vertical and you are not focused correctly, you see two lines, indicating a need for better focus.
If it is horizontal, you see a single horizontal line, as both your points of comparison are on the same plane (if you could see the outer edges of the line, you'd notice the edges do not align). So what do you do?
You tilt the camera until you can see the ghosting clearly, focus and tilt back.
You are absolutely right, that turning 45° can be beneficial. That's why DSLR focus sensors had horizontal, vertical and diagonal sensors on them.
And considering things like fabric, where there are basically lots of tiny squares, having those diagonal sensors can be absolutely essential.
That's pretty much why canon is for sure still working on getting quad pixel af ready.
Splitting the pixels into groups of four will allow to detect differences between two horizontal and two vertical subpixels, but also compare the diagonal pixels to each other.