Natural for whom? The computer?
Remember that we're talking about an external interface here -- the question is in what units would a user of the timer facility want to specify a duration? Virtually nobody measures time in binary units; we all think of time in milliseconds, nanoseconds, etc.
The Unix time_t type (which I think is what you're referring to as the Unix clock) doesn't actually figure in anywhere here -- this is a value that specifies a duration, not a point in time; and if it ever gets added to a point in time, that time is in the kernel internal format, which is a count of clock ticks.
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