The executable files (PE format on windows) cannot be used to boot the computer because the PE loader is not in memory.
The way bootstrapping works is that the master boot record on the disk contains a blob of a few hundred bytes of code. The BIOS of the computer (in ROM on the motherboard) loads this blob into memory and sets the CPU instruction pointer to the beginning of this boot code.
The boot code then loads a "second stage" loader, on Windows called NTLDR (no extension) from the root directory. This is raw machine code that, like the MBR loader, is loaded into memory cold and executed.
NTLDR has the full capability to load PE files including DLLs and drivers.
