Removing the secondaries is easy to do, but not required. When the dealer installs the TOR pipes they should load an OEM Triumph tune for them. This is different to the stock tune in that it is a little richer. However, it doesn't remove the restrictions in the first three gears.
However, that is easy to do with TuneECU. When you get the bike home, use TuneECU to read the tune, then save that tuning file. Then edit the tune to open the secondaries 100% in all gears and at all throttle positions - then save that tune with a different name. Then load that tune into the bike. All is done.
Another alternative is to get a better tune off one of the chaps on this site and load that into your bike. Make sure you specify the model and year of your bike, as well as which air filters and exhaust you are using if you are requesting a tune.