Lenovo Yoga 12.5" Touchscreen Ultrabook

Does this come with the Wacom pen?

Includes the Thinkpad Digitizer pen.

Do you know if the i3 model here:

comes with the digitizer pen?

Likely not, as it isn’t listed. But, bigger surprises have happened; you might get one anyway. As a minimum, you’ll receive what’s “In the box” on the Specs tab.