Ever thought it just may because the default scaling/resolution is MICROSCOPIC and you're giving yourself a headache after 15mins of trying to read it?!
This was actually a part of what I was thinking when I returned the tablet, and that motivated me to get the R7 (15in). The only difference between Acer R7 and Surface Pro 3 seemed to be their sizes.
On the other hand, I don't stare at the small fonts of the window tabs, for example for a long time, and mostly I only read my own writing which would have similar sizes in all Note 10.1, Acer R7, and Pro 3.
Also, I wouldn't have similar problems reading even a paper book with even smaller font, so it is hard to say that the small fonts soley cause the problem.
Both R7 and Note 10.1 still cause eye strains if I had been working on it throughout the entire day. Hours of staring at a monitor is not healthful for my eyes, and it would be the same for anyone. (Maybe Kindle would cause less eye strains but one can't write on it). But with Pro 3 I was bothered within 15-30 min.
But it is not a headache. It is a tingling sharp disturbance only in the particular part of part of the eyes, like somewhere behind the "Lens" part of the eyes, and then I got red, swollen eyes when I still continued. I don't think I had any headaches while using the Pro 3
I can't tell whether the reasoning regarding the PWM actually works because I never tested at 100% intensity and I don't have the Pro 3 with me anymore. If the problem disappears when I use the tablet at 100% intensity, it was probably the PWM..