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While I'm not sure what the advantage is, I think this is the reason for it in ROS 2.

builtin_interfaces/msg/Time is part of the builtin_interfaces package which contains "message and service definitions for types defined in the OMG IDL Platform Specific Model".

In section 2.3.2 of the OMG DDS 1.4 spec the Duration_T and Time_T types are defined:

The two types used to represent time: Duration_t and Time_t are mapped into structures that contain fields for the second and the nanosecond parts. These types are further constrained to always use a ‘normalized’ representation for the time, that is, the nanosec field must verify 0 <= nanosec < 1000000000

and a little lower down

 struct Time_t {
     long sec;
     unsigned long nanosec;
 };