.NET Micro framework is actually a different beast in that's it's close to the metal but it's not compiled to a specific architecture. The MF is a bytecode interpreter vs the mainline dotnet framework which is JIT'd or AOT compiled (with NGEN).

This approach gives a couple advantages and a couple disadvantages. Specifically, the advantages the debugging and reloading can be done extremely quickly, the bytecode is small thus giving a lot of functionality per the byte of storage space, and it's significantly easier to port from microcontroller to microcontroller. Downsides, it's pretty slow - typically the heavy lifting happens in the HAL/MF, and you can't write interrupt handlers directly in it - although you can indirectly via the managed driver interface.