JQL search results are generally fetched directly from the Lucene index, which stores timestamps with only millisecond resolution, whereas fetching the actual issue gets the date directly from the jiraissue table in the database, which can have sub-millisecond resolution (at least depending on your configured database).
EDITED: I see that I misread the precision above: the timestamp returned by getting the issue returns only milliseconds (vs nanoseconds) and the JQL query returns only integer seconds (vs milliseconds), so the Lucene data type linked above is not relevant.
However, the answer is still the same: JQL gets the result from Lucene, while an issue fetch gets the value directly from the database. On further investigation of why the Lucene index is not returning milliseconds: in the JIRA source in BaseFieldIndexer.indexDateField, JIRA calls LuceneUtils.dateToString(date) to convert the created field into a value that is indexable by Lucene. The dateToString method explicitly converts the field into an integer number of seconds (lopping off any milliseconds in the process), and it then converts the number to a String representation for indexing purposes.
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