I think probably the most stark difference between access logging in JIRA and Apache's logging is that JIRA will tell you which user performed which action, whereas Apache will only tell you the IP address of the client at best. JIRA's access logs also tell you about which pages are being accessed and from there you can ascertain exactly what actions are being performed, which again isn't as explicit in Apache's HTTP logs so generally I would recommend using the JIRA access logging over Apache's.
All the best,
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