In Dr. Vince DiMiao's book on forensic study he discusses how to recreat a shooting using the powder burns. According to the type of powder etc, and testing, it can be determined how far you are from the person you shoot. This evidence can backup your story. There are a number of ways a forensic expert can recreate your shooting by testing the cartridge you were carrying. Generally, reloads are not considered as accurate for this forensic study because they never know how much powder you put in each cartridge etc.
With factory ammo, this evidence can more easily be used in your favor, (or against you I suppose, if you were lying about how that shooting went) because the examiners will use that factory ammo to recreate the scene. Reloads cannot so easily be used for evidence because there is no official quality control there and they have no idea if every bullet is the same. IOW, if they want to guage your distance from burned clothing, they take a round and shoot it at some clothing and measure the burns. From this data they can figure out how far you were from the target. If you are using reloads, then it makes it rather sketchy to take some more of your reloads and shoot them and test the burns, because they really don't know if the reloaded cartridges they are testing are exactly the same as the ones you were carrying (was there more or less powder, a difference type of powder etc?). So, feasibly, factory ammo could more easily be used by examiners to recreate the shooting and this could work in your favor (or not?). Personally I would make a batch of defensive ammo and label it clearly if I were going to carry reloads for defense.
As far as people being prosecuted for using "super ammo": Ayoob tends to rant about this, but his case studies are weak. He claims that you will be hung out to dry, but he only gives one or two examples of reloads being brought up in court, and in all cases the shooter (good guy?) got off. So, apparently, even if it were brought up that you carry reloads, there is NO evidence that it will matter. To my knowledge, there has never been a single legal case in history where it worked against the shooter that he was using reloads, and it made him lose his case and be prosecuted.
IMO, this is nothing more than a popular gun shop myth. And, one reason it is so popular is that gun shop owners and ammo companies make money off of convincing you that you have to spend a dollar per bullet for you ammo. It is very common that I hear this myth from gun shop people (among many other myths) and I have to wonder if they don't tell it just to get you do buy some expensive ammo from them.
In one case that Ayoob cites, a man used reloads and the lawyer accused him of making deadly super-ammo. So, they tested the velocity on some of his loads and found that they are at the same velocity as other loads on the market, and it came out as no big deal.
This case study not only shows that it is far from proven that it will be successfully used against you in court if you use reloads, but it also shows that examiners are willing to test reloads and trust that they are the same (how do they know that all the reloads in his magazine were loaded to the same velocity?)
That is my reading on the subject and by no means any expert advice. I carry factory ammo most of the time, but occasionally I carry reloads and have no problem with it.