I have no idea about what you mean by "making up for a lack of a RTC" as all pxa chips ship with a propper RTC
what you can do is write to the real time clock interface in the proc susbsystem that will susequently enable and activate the on board alarm to wake the device at a specified time,.
all it does is turn on the device, however if a userspace program polls the clock every second then the alarm should trigger, and as long as it dosent mind gaps of more than a second between polls then it should be fine
you second point: The kernel can wakeup and sound an alarm, if no other script listed in /etc/apm/alarm.d takes over. is somthing that no kernel should do. what it should do IMHO is run a preregistred user space program (like how hotplug regiseters itself throgh the proc interface see /proc/sys/kernel/hotplug)