Not always (raise your hand if you've had an unbootable system due to a broken or insufficient initrd).
In retrospect, the whole concept of the initrd seems like an enormous kludge that was thrown together temporarily and became the permanent solution.
Eh, kinda. That's where "essential" .ko modules are packed into - those that system would fail to boot without.
Alternative is to compile them into kernel as built-ins, but from distro maintainers' perspective, that means including way too many modules, most of which will remain unused.
If you're compiling your own kernel, that's a different story, often you can do without initrd just fine.
It's a lot simpler to merge them in a directory that can be mounted across multiple machines than have four separate mountpoints.
Nearly every shell script starts with "#!/bin/sh", so you can't drop /bin. Similarly, nearly every python script starts with "#!/usr/bin/env python", so you can't drop /usr/bin.
Hence symlink.