It doesn't make sense, no. The whole article seems very barebones - I'd have expected to see discussion of how the sensor-lens system needs to work for proper focus, at least. Granted they link the STL for their case, which will be designed for correct alignment, but some discussion would still be useful to those wanting to mod for different lenses or sensors.
Correct, the MTF of a lens is meaningless unless the lens and sensor are aligned (aka focused) correctly. Contrast in the image is directly related to the square-wave geometrical MTF. Once you factor in focus/alignment error, it can be difficult to tell the difference between a "3MP" and "12MP" rated lens. We're talking about <10 micron accuracy.
This is why companies like Apple use 6-axis active alignment machines to manufacture every camera module.
The "Megapixel" rating of a lens is based on the nominal as-designed MTF and image sensor Format. There's a lot of manufacturer fudging that goes on with these ratings. And some in China literally print whatever they want on the side of a lens. I've seen the same lens with both "3MP" and "5MP" printed on it.
