Now I understand better what you were doing.
I agree that -filter LanczosRadius -define filter:lobes=8 -distort Resize is a reasonable low pass filter that would emulate FFT processing reasonably well.
Let me suggest something, without really knowing how well it will work. This being said, you probably know most of this already.
If you specify a filter (with a recent version of ImageMagick), the short circuit that bypasses the filtering when resizing at exactly the same size will not be turned on.
So, for example
convert Harper_window_crop.jpg -colorspace RGB -filter Jinc -define filter:window=Box -define filter:lobes=8 -distort Resize 100% -colorspace sRGB Jinc8.png
applies a "raw" Jinc-windowed Jinc 8-lobe filter with cutoff frequency matching the Sinc's, to the image without resizing, and
convert Harper_window_crop.jpg -colorspace RGB -filter Jinc -define filter:window=Box -define filter:lobes=8 -define filter:blur=2 -distort Resize 100% -colorspace sRGB Jinc8blur2.png
will apply a similar filter, except that the cutoff frequency is half the corresponding Sinc's.
You can play with blurs that are given by floating point numbers (e.g. blur=1.414213562373). Also, if you want Jinc-windowed Jinc, all you have to do is
convert Harper_window_crop.jpg -colorspace RGB -filter Lanczos -define filter:lobes=8 -distort Resize 100% -colorspace sRGB JincJinc8.png
Also: When the number of lobes is large, LanczosRadius is pretty much the same as Lanczos. And you can replace RGB by XYZ. I think recent versions of IM do XYZ pretty cleanly. But it should not make much of a difference, because there basically is not truncation error when using -distort Resize, and the correspondence between RGB and XYZ is affine (I believe), and we are applying a linear filter (and I'm using an HDRI, that is, floating point, version of IM).
I'd give a shot to Lab, why not? And actually, I'd consider processing the Y channel of XYZ differently than the X and Z ones (use a less blurred version).
I gave a quick try to the above, and the results are underwhelming. But I figured I'd pass the idea along.