A suite of data format standards will achieve all this without having to resort to a (hand-wavy) half-baked notion of standardized set of data processing module

A suite of data format standards will achieve all this without having to resort to a (hand-wavy) half-baked notion of standardized set of data processing modules (aka “applications”). And we’re already doing this, and I am certain the OP has also modified data created by one application with an entirely distinct other application. Overall, OP fails to provide a lucid and compelling reason for speculating about a half-baked notion that supposedly solves some poorly defined problem. (Repeat: interop is optimally done via data translation. Local coupling that allow for eco-systems of loosely coupled (via data) applications.)