Hi Shivendoo ,
just some comments
not sure about MS Recommendation , but i had large scale implementation where we enabled the Modified/created by,Date time for all tables in the system ( apart from Temp table, and disabled table ) and we never get an a performance issue ... and as i understand such information is very helpful for the business not to mention the auditing side
its not big development work , you can enable these properties by code ( i have an x++ script , loop over the table to set these properties in , and it takes 20-30 mins to run and 20 mins to Sync the DB ) it its couple of hours work ( let me know if you need it :) )
about the custom applications , we cant evaluate the risk until we know the details of each app . (tech , Data set , data size , Recurrence .. )
about the change tracking could do the same ... but i suggest to keep the changes from AX side , so you are maintaining the application tier not the DB Tier ,