So a tried and true approach -- but remember, this is a long chain of details that matter, and we are only as strong as the weakest link -- is to mount the Power Commander for the dynamometer run, ensuring it is zeroed before the run, then have the operator connect to the DynaJet and do the run, loading the resulting trim tables on the Power Commander.
Then remove the Power Commander, and connect to a computer with the DynaJet control software (free download from their site), and download the trim table from the Power Commander. Then send your map along with the trim table to someone with a special version of TuneECU who can combine the two, and return to you a new, tailor made for your bike, base map. Then put the Power Commander on the shelf until you make another major change to the air/fuel/exhaust path, and need to repeat the process.
To your question, my understanding is it is best to start with the STOCK OEM map that was delivered with the bike (or last one updated by Triumph).
Your needs, your results, may vary.