Cunic inch and injector size is for the purpose of scaling the VE tables. Raising cubic inch is going to add fuel across the board. Making injectors smaller is going to do the same. SE wont let you get to the correct injector size. So, the tuners choice is to go a bit big. (lean out entire cal) or to be a bit small. (richen across the board) Cubic inch is much easier to deal with because if you do run out of head room in the VE table. You can add 10% to the cubic inch and take away same % of VE tables you are still in the ball park. There isn't a rule of thumb like this on the injector size. At the same time. What ever % the cubic was raised over original can be taken away from the warm up enrichment, and this % can be used to get accel and decal in the ball park.
You do have some 117's and some cubic inch can be taken out but is it worth the time and effort to maybe drop it 5? I don't think so. EGR tables would probably help address some of this, but that isn't an option with SE. Your sheet is right in line for the 259E cam. So, I would say it is what it is and the tuner did what he needed to do.
The warm up table doesn't seem like it has enough out by looking at the cal, but that doesn't mean that it is rich on warm up. Does it smell like fuel on start up, black smoke. If no. Enjoy the thing. Other thing I noticed is: EITMS is turned off. I would suggest tuning it on. If the bike is tuned correctly and you don't parade the thing. It shouldn't be a factor.