To recap: The slanted edge method projects image intensity values onto the normal of the edge to produce the Edge Spread Function (ESF). Any practical implementation has to place an upper limit on the maximum distance that pixels can be from the edge (as measured along the edge normal). MTF Mapper, for example, only considers pixels up to a distance of 16 pixels from the edge.
Looking back at the Airy pattern that results from the diffraction of light through a circular aperture we can see that the jinc2 function has infinite support, in other words, it tapers off to zero but never quite reaches zero if we consider a finite domain.
We also know that the effective width of the Airy pattern increases with increasing f-number. Herein lies the problem: a slanted edge implementation that truncates the ESF will necessarily discard part of the Airy pattern. The discarded part is of course the samples furthest from the edge, and we know that those samples tend to contribute more to the lower frequencies in the MTF.
Simulating a slanted edge image using the Airy + photosite aperture model, with an aperture of f/8, light at 550 nm, a 100% fill-factor square photosite aperture, and 4.886 micron photosite pitch (something approximating the D810), we can investigate the impact of the truncation distance on the MTF as measured by the slanted edge method. Here goes:
If we compare the red and the black curves we can see that a wider truncation window (red curve) reduces the overshoot at low frequencies. If we had the opportunity to use an even wider truncation window, we would be able to reduce the overshoot to even lower levels.
Lastly, if we introduce apodization into the mix we are compounding the problem even further by attenuating the edges of the PSF. This leads to even greater overshoot (at low frequencies) in our measured MTF curve.
Bottom line: The slanted edge method is constrained by practical limitations, most notably the desire to have a finite truncation window, and the desire to reduce the impact of image noise using apodization of the PSF. These constraints lead to overshoot in the lowest frequencies of the measured MTF. It may be possible to apply an empirical correction to minimize the overshoot, but only at the cost of making strong assumptions regarding the shape of the MTF, which is best avoided.