Macbook Pro 2016 (15") has weird default Resolution
The 2016 15" Retina MacBook Pro has a resolution of 2880 x 1800. 1050/1800 and 1680/2880 are both 7/12 which means it is scaling properly for 7/12 the maximum resolution.

I'm not sure how the resolution or scaling would cause you to have headaches unless the text and images on the screen legitimately appear blurry. Is that the case? It is possible that you have the screen brighter, or glossy rather than matte, or are using it differently, but I can't really say.

In general, you should take short breaks every 10 or 20 minutes and have a screen brightness that matches the ambient environment (many people make it too bright which forces them to squint or tense up and get headaches) to prevent eye strain, and remember to blink frequently to prevent dry eye.

Short of that, I'd say change the resolution to whatever feels better for you, or see if anyone you know would be interested in trading laptops if you find theirs to be easier on your eyes.