AA filters are used to prevent digital artifacting, the most obvious of which is moiré, but also includes things like stair-stepping. the only way to make AA filters obsolete is by making the spatial resolution of the sensor high enough, i.e. high pixel density.
MFDBs do not have AA filters because the manufacturers can't afford to make them, not because it's the intelligent engineering decision. I bet Fuji opted to only fix moiré and not any other aliasing in the Pro1 because photographers obviously like having false detail, thinking it's evidence of better sharpness and resolution.
if you want to know more, look up aliasing or study digital signal processing.