Yes HotRod you can / they can do this and that is what I have already done. however what I am missing is 2 settings / configurations options that Mobe is seeing from within the software that came with my purchase 4 moths ago. I am presuming that his software also came with his race tuner.
I would like to make the modifications that he (Mobe) has already tinkered with, but I don't have the options from within my software.
HotRod
Before they install the software and dyno tune your bike make sure you get a dyno sheet that includes air / fuel ratios in SAE format not Standard and done in 4th Gear NOT 5th. Personally I would want smoothing at no greater than 2 (can go as high as 5 with dynojet dyno) so you have an accurate picture of how well the dyno tuning has helped you.
I have many many custom maps for the SE 103 from a very rich one to a very lean one as well as many of the changes we made along the way just to give baseline for making changes on my own.
Hotrod, if you're buying the race tuner make sure that they give you a copy of the Map in MT5 format that they make for you for your bike. This will enable you to make changes or bring it somewhere else if you ever want to modify it again and not have to start from scratch.
Best of Luck with your Tuning

We look forward to seeing your Dyno Sheets of before and after