They do run hot, but they don't have to run as hot as they do from the factory. HD has to run them that way to meet EPA standards, and EPA is not to blame, HD is, for not offering up a better solution (water cooling) 4-5 years ago. It's not like the EPA standards were a big surprise, after all.
A good tune will HELP, but not cure, the heat issues with a 110" air cooled motor. However, I would seriously question a dealer installed "base map" to even be close to a better tune than stock. I do not trust anything HD dealers do with regards to tuning a bike properly...there are exceptions of course, but I'd venture to say that 80% of dealers blow smoke up the customers azz, don't have a well trained tuner, and just do "stuff" to get the customer out the door with the bike running half-azzed right.
IMO, the Fullsac Stage I with the TTS is by far the best system for getting the bike 90% where it needs to be, for the least amount of money spent. Steve has tuned countless bikes with his system, so his "base map" is, again IMO, going to be much closer to right than something a HD dealer sticks in the ECM. And with a little tweaking, the owner can dial it in further if needed/wanted. It's just an easier row to hoe. But it's not what everybody wants. I just want to do things to my bike that require the absolute minimum involvement by the dealer...but, I can do a lot of things to my bike myself, and not everyone is so inclined.