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I see "fo:table, table-layout="auto" is currently not supported by FOP" warnings in my log, but the PDF documents look good.

Those warnings don't have any effect. You can safely ignore them. (These will not appear when using modern version of the app.)

If you prefer not logging those warnings, then add the following lines to JIRA_HOME/atlassian-jira/WEB-INF/classes/log4j.properties and restart Jira: 

########################################
# CLASS-SPECIFIC LOGGING LEVELS
########################################

## ... there is stuff defined here, leave that unchanged and add these 2 lines to the end of this section

log4j.category.org.apache.fop.fo.FONode = ERROR, console, filelog
log4j.additivity.org.apache.fop.fo.FONode = false

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