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I agree that the old hybrid technology which has now evolved into the multiple chip on a single carrier technology could have advantages. It would for one allow the whole system to be put into a single shielded package with improved EMI performance. Taking up silicon area to just mount the filter would be very expensive as the filters are many times larger than the silicon circuit.
The stacking method could further shrink the size.
As historic interest, the three dimensional IC was discussed in a sophmore level transistor textbook in 1957. We have yet to find economic ways to make them.