Very rarely would we take off with the packs off. Generally in mild climates such as western Europe there would only be a couple of days a year (if your lucky) when the temperatures would be such that you would need the increased performance or reduce the risk of getting an EGT exceedance. In the middle east, Africa and say the hotter parts of Southern Europe then it would be a regular occurence.
The basis way of determining the tabulated flex temp is to enter into the performance tables for the runway in use and find your take off weight. You would have your planned take off mass from your flight plan. We note down a series of weights and the associated flex temperatures and speeds in and around this planned take off mass. When the actual load sheet is delivered to the aircraft we can then select a tabulated flex temp which has a take off mass that is greater than the actual one from your loadsheet. To arrive at the corrected flex temp which you enter into the MCDU you need to correct for air conditioning (taking off the minus 3 you stated), pressure, and engine and engine/wing anti icing if they will be used. In the case of a wet runway then additional corrections will need to be made for this as well as to the V speeds.