Historically, C compilers really did run an assembler in a separate process and communicate with it via pipes or files. gcc still ships with gas. gas is more oriented to the needs of a compiler than to human writers of assembly code.

Some compilers emit machine code from their own low-level intermediate representation, though. The trade-offs are similar to any other build/buy technical decision: full-custom gives you more control, while forcing you to reinvent the wheel.