Tuneboy is just a program and a cable that allows you to download tunes into the ECU. The Tuneboy web site has all the standard tunes, including for the R3T as well as custom dyno tunes that Wayne at Tuneboy does on R3's with various exhaust and intake configurations. You can always try something and then go back to the standard tune. If you go to the Tuneboy web site, you will see there is a custom tune (20256_1) for the R3T with TOR pipes with the snorkel under the seat removed.
For the standard R3, there are tunes for TOR/cat bypass, jardines, unifilter intake, etc. There is no custom tune for a 3 into one into 2 (D&D). The Jardine (also 3 into 1 into 2) tune would probably be too rich. If you can find a good dyno tuner, you can create your own tune specific to your bike. Tuneboy also allows you to transfer a PCIII trim map into a tuneboy tune which you then load into the bike. Pig9r used to offer renting his PCIII out for this purpose. Since most dyno tuners are familiar with the PCIII, this is a good practical alternative.
By the way, your dealer probably loaded the standard TOR/cat bypass tune. How is that working? All of the standard tunes close the secondaries to various extents to limit power. Tuneboy allows you to open them 100% in all gears & rpms.