A pair of strands of fiber optic pass messages between my network switches but doesn't imply that they have any intelligence.
Let's examine your hypothetical machine. Your applications have no idea when the drive should spin down. One application could assume that it knows when it won't be accessing the drive anytime soon and issue a shutdown command, but then another application that is actively using the drive gets screwed. So your applications don't actually know, unless they all participate in a common system to cooperatively manage the drive. In computer science we call a metalayer that manages shared access to an I/O resource an "operating system."
Your operating system can have knowledge of when the last time a drive was accessed and could use historical patterns to guess at future access patterns, or could actually have a formal API to allow applications to indicate what'll happen next. UNIX, however, has never really done a formal job of this. Kernel designers have deemed it a userland problem, making it difficult for designers of laptop OS distributions to do a good job of power management.. well anyways, a bit off track.
In the end, UNIX kernel developers have largely avoided trying to broker drive spinup/shutdown in the kernel or syscall API.
The drive itself is a fully intelligent device, containing its own processor and operating system, able to monitor its own health (SMART), queuing and handling multiple outstanding requests (NCQ/TCQ/etc), automatic error recovery and sector remapping, etc., etc., etc. It is an intelligent processor dedicated to the management of the physical drive. To say that the HBA - a pretty stupid bit of hardware - knows better when to spin the drive down than the drive's controller is a bit odd.