If the dealer loads your EFI calibration with a SE EFI custom calibration Cartridge which is how it comes from the factory or when the dealer does a Stage I,II, 1550 etc. flash, for $150 (see p 452 of the 2003 book) a stock part number is stored in your ECM. If you then buy and use the SE Tuner and load a calibration from the SE Tuner CDROM the dealer will absolutely know as the stock number in your ECM will be irrevocably changed by the SE Tuner to 32107-000. However if you can convince your dealer to load an SE Tuner calibration from the CDROM then you can mess with that calibration using the SE Tuner and the number does not have to change. However you should change the extension to something like 32107-006 to document what you did. Once the SE Tuner number 32107, overrrides the SE cartidge number in your ECM it is not possible for you to change it back and 'fool' your dealer into thinking you did not use the SE Tuner. The part number change is irrevocable to the EPROM in the ECM. However the dealer can flash you back with a SE cartridge for $150. If you have a very good rleationship with your dealer tech (and he knows the EFI Tuner) then they might work with you to improve the SE Tuner CDROM calibrations - and believe me they can be improved - then you would want to use the -000 extension to document each improvement.
P.S you can't tune it right without an EGA for CO and Airfuel as the HD Delphi EFI system is open - loop. No O2 sensor in the exhaust manifolds so you will need one - preferably a dual probe as these cylinders get independently adjusted.
I run a 2002 FLHTCUI 1550 Stage I and it has had eight different SE Tuner calibrations to get the best for my riding traits. Torque now at 90.5 at 3050.