I bought my 09 Ultra used, so don't know if any thing has been done to lower it but I havent seen a lowering kit on it. I put one on my 98, so know what to look for.
The seat doesn't seem to be modified either. The staples all seem original so here is the thing I find odd here.

I am only 5'8" with a 29/30 inch inseam and I am flat footed when I stop my Ultra.

 

The reason why they do it with such ease is probably cause there's about a 500 pound weight difference between touring bikes and sport bikes. The lower center of gravity of touring bikes makes it easier but when a sport bike starts to tilt you can easily right it up. When an 800+ pound bike starts tipping, LOOK OUT!

 

Hey guys, sorry it took a while to get back on. Solved the issue....it was definitely technique. I got spoiled on my sporty and softail and stopped using my front brake while lowering both feet on the ground...was not an issue. Watched a few videos on youtube and learned to stop with back brakes and left foot down. Takes some getting used to breaking old habits....but it works for me! I feel like such a newb. haha

 

You are and I mean no disrespect there, I'm 5'8" with 30.5 inseam and I can flat foot my Ltd. BUT that's not the issue, you are half way there having learned to generally use the rear brake at lower speeds to a stop. However instead of putting your left foot down work on which foot is actually best for any given situation. In the main right foot down is better as it allows instant use of the gear lever, neutral a lights into gear and away instead of either sitting there burning away or having to shuffle legs.

Scenarios, pull up to a junction to the turning left then generally the left foot down will be better and vice versa with right hand turns. Hill starts for newb's are generally better on the back brake so left foot down then.

Enjoy your ride

 

I'm only ltl over 5'8" 175 lbs with less then 30"inseam and I ride 07 UC stock everything suspension vise, it was iffy first but after 80K + miles I don't feel it too heavy or too tall for me.My wife and one of her friend also ride 08 UC but lowered both ends my wife is same height as me but friend she is only 5'4" both ride real good after taking the Ride Like Pro class and lots of empty parking lot practice.So all it's practice and more practice to increase your confidence and skill.