long_query_time description says:

VARIABLE_COMMENT: Alias for log_slow_query_time. Log all queries that have taken more than long_query_time seconds to execute to the slow query log file. The argument will be treated as a decimal value with microsecond precision

while for log_slow_query_time it says

VARIABLE_COMMENT: Log all queries that have taken more than log_slow_query_time seconds to execute to the slow query log file. The argument will be treated as a decimal value with microsecond precision

So, the old description refers to the old name, and the new description to the new name. It is not entirely illogical, but it would be probably even more logical if the descriptions for aliases were identical (except for the "Alias for ..." part), and the description for long_query_time used the new name.
Alternatively, they could use no name at all, and refer to themselves as "this value" or alike, some other descriptions do so.