I'm not sure what clarification I can provide beyond what it says in the text, which is pretty explicit. For instance, towards the end of Section 8.5 it states, "The first three test programs in this project assume that the bootstrap code was not yet implemented, and include test scripts that effect the necessary initializations 'manually'. The last two test programs assume that the startup code is already part of the VM implementation."
Each of the first three test programs also consists of a single .vm file. For each of the other two it says something like, "Since the overall program consists of two .vm files, the entire directory must be compiled in order to produce a FibonacciElement.asm file"
Could you please be more specific about what the point of confusion is?
You might look at the authors website.
https://www.nand2tetris.org/project08They basically say the same thing, but I think their verbiage and terminology is a bit cleaner and more precise.