To answer your questions, please note that this is subjective as there are different processors, different platforms, different assemblers and C compilers, in this case, I will talk about the Intel x86 platform.
- Assemblers do not compile to pure binary, they are raw machine code, defined with segments, such as data, text and bss to name but a few, this is called object code. The Linker steps in and adjusts the segments to make it executable, that is, ready to run. Incidentally, the default output when you compile using gcc is 'a.out', that is a shorthand for Assembler Output.
- Boot loaders have a special directive defined, back in the days of DOS, it would be common to find a directive such as
.Org 100h
, which defines the assembler code to be of the old .COM variety before .EXE took over in popularity. Also, you did not need to have a assembler to produce a .COM file, using the old debug.exe that came with MSDOS, did the trick for small simple programs, the .COM files did not need a linker and were straight ready-to-run binary format. Here's a simple session using DEBUG.
1:*a 0100
2:* mov AH,07
3:* int 21
4:* cmp AL,00
5:* jnz 010c
6:* mov AH,07
7:* int 21
8:* mov AH,4C
9:* int 21
10:*
11:*r CX
12:*10
13:*n respond.com
14:*w
15:*q
This produces a ready-to-run .COM program called 'respond.com' that waits for a keystroke and not echo it to the screen. Notice, the beginning, the usage of 'a 100h' which shows that the Instruction pointer starts at 100h which is the feature of a .COM. This old script was mainly used in batch files waiting for a response and not echo it. The original script can be found here.
Again, in the case of boot loaders, they are converted to a binary format, there was a program that used to come with DOS, called EXE2BIN. That was the job of converting the raw object code into a format that can be copied on to a bootable disk for booting. Remember no linker is run against the assembled code, as the linker is for the runtime environment and sets up the code to make it runnable and executable.
The BIOS when booting, expects code to be at segment:offset, 0x7c00, if my memory serves me correct, the code (after being EXE2BIN'd), will start executing, then the bootloader relocates itself lower down in memory and continue loading by issuing int 0x13 to read from the disk, switch on the A20 gate, enable the DMA, switch onto protected mode as the BIOS is in 16bit mode, then the data read from the disk is loaded into memory, then the bootloader issues a far jump into the data code (likely to be written in C). That is in essence how the system boots.
Ok, the previous paragraph sounds abstracted and simple, I may have missed out something, but that is how it is in a nutshell.
Hope this helps,
Best regards,
Tom.