MacOS – view tab in safari not allowing actual size choice

Turns out, there's a Preview preference that controls what actual size actually means:

If you want points to correspond directly to physical pixels, choose the first option.
(Not sure how it affects Retina displays though!)

I switched from a DVI-D dual link DVI input, to DisplayPort Input. The monitor supports HDMI, DVI, DP and analog inputs.

OS X was able to determine the screen DPI on DP. I open a PDF and choose View/Actual size, the size looks right now.

I do not know why DVI does not work. I can provide the ioreg if anyone is interested to investigate further.