Within the population order, there could be a new stage that gets executed between the base terrain generation and decorating that terrain. This new stage would place TS scripts (similar to how trees / structures are handled) on to the basic generated terrain, then any blocks placed by said scripts would be treated the same as terrain generated via noise equations, with palettes and other post processors applied.

Initial terrain determined by biome noise-equation

Script based terrain placed over terrain

Script and terrain merged together

Population, palettes, etc.. applied to the above terrain

This functionality is superseded by pack defined generation stages