I'd expect MIRI to build the "proper reasoning" layer, and then the AI would use its "proper reasoning" to design fast heuristic layers.

One example of a very-hard-to-avoid layering would be if the AI were distributed over large areas (global or perhaps interplanetary), there would probably have to be decisions made locally, but other decisions made globally. You could say the local processes are subagents and only the global process is the real AI, but it wouldn't change the fact that the AI has designed trustworthy faster less-accurate decision processes.