Regarding the WB clock program, I'm fairly sure it only compares the system time to an alarm time (in memory) and alerts you. Since the alarm output from the RTC is not used at all, I doubt the clock program sets the hardware alarm.
Programming the RTC is easy enough, the
datasheet gives all the register details you need, so it's just a matter of writing a small application to take the alarm time from the user and set the registers accordingly. You could even do it in Arexx/RexxMUI if you wanted to be lazy.
The interface to the ATX power supply is another question. I'm not sure of the behaviour of the RTC alarm output. It's open collector, so will obviously sink any current on the output in alarm state, but no idea how long for. Not sure how the ATX power supply wants it's "off" signal either. You might need a transistor or relay to interface the two to avoid logic level clashes or whatever.
As for HDD head parking, if your disk is less than about 20 years old, it'll do this automatically. Manual head parking for voice coil actuator disks is equally as useful as screensavers for LCD monitors :-)
Unless your HDD is about the same size as a small ocean liner and uses stepper motors to set the head position...