This help page documents the fields displayed in Web-based log views vs. downloaded log files:
The reason for that discrepancy is because the downloaded file format has had to remain almost exactly the same for legacy support of preexisting client integration methods that depend on it, whereas we at least have more freedom to add information and improve comprehension in the Web-based view.
That empty Column Z in the downloaded log file is for an obsolete field, "Affiliate Share (common for txn)" that is only relevant to transactions from 2008-11-07 to 2010-05-30. Before and after those dates, all affiliate earnings are only reported in Column AH, "Affiliate Share (per item)", so for log queries outside that date range, Column Z is retained for legacy compatibility but left blank. The reason for that blanking and the field's obsolescence was to avoid confusion about just where affiliate earnings are actually reported.