1) On vector, this wouldn't work because features are serialized on the fly. Additional runs incorporating new data or data in a new order would use different encoding names which would result in incongruities during the bind phase. The base map functionality is the closest to an intermediate vector state as the IMC will go.
On raster, this is beyond the scope of the application. The regular raster toolkit (Tier3) is intended for production environments. IMC saving intermediate raster states would be impractical both from the practice being beyond the technical capabilities of many of its users and the toolkit being required to bind the intermediate files together. Any functionality similar to this approach would be added into the regular toolkit (e.g - deconstruction into major blocks).
2) The IMC limits command line arguments by design. The complexity of the many project settings make the usage of command line arguments impractical. Adding command line arguments for project variables bloats the design, adds additional points of failure, and circumvents the designed methods of control.