I like most of what Ayoob has to say on self defense related topics but he's way out to lunch on the "don't use handloads" issue, or at least badly taking it out of context.
The only case I have ever heard where this was an issue was a case related by Ayoob where he was an expert witness for the defense. The case involved the wife of a handloader who shot herself with a .38 Special. The investigating officers confiscated *some* handloaded ammo and then based on forensic testing of *that* ammo determined that the evidence did not support a suicide.
The problem was that the wife shot herself with a target load that left comparatively little powder stippling at the short range necessary for a suicide. The self defense load that the officers found in the room and confiscated for testing, left a similar amount of stippling at a much longer range, and they thus concluded the husband had to have shot her.
The problem here wasn't hand loaded self defense ammo, the problem was having two different types of ammo. Ayoob did a good job of demonstrating that the ammo in the gun was not the same as the ammo confiscated, created reasonable doubt and the husband was aquitted.
----
The take aways from this need to be:
1) Regardless of whether you use factory self defense ammo or handloads, you need to ensure that you keep your self defense ammo separate from your other ammo and keep it clearly marked as your self defense ammo.
2) If you do use hand loaded self defense ammo, you need to also ensure that you leave enough in the box to allow for forensic testing for velocity, powder stippling, etc.
----
The value of a forensic database of factory ammo is in helping to identify what an unknown shooter may have been using, and thus helping to connect a suspect to the crime if ammo is confiscated in the course of arresting a suspect. In a self defense shoot, there isn't a question that you shot someone, so there is no need to try to identify a type of ammunition. There is potentially a need to verify your story by matching it to the ballistic evidence, which is where it is important that the police are able to properly locate, identify and confiscate the correct carry ammo to do that ballistic testing to verify your account of the events.
And again, that applies to both factory ammo and handloads.
-----
As to a prosecutor trying to paint you as a gun nut building extra deadly rounds to kill people, in the real world it's either a good shoot or it isn't and handloading your own self defense ammo isn't going to turn a good shoot into a bad one - unless you are doing something incredibly stupid like making explosive bullets, etc.
The argument can also easily be turned around. For example, I use Hornady 125 gr XTPs on top of 9.0 grains of Unique in a .357 Magnum case. The bullet gets about 1250-1300 fps in a 3" barrel and at that velocity gives very reliable expansion to around .55" and penetration just under 18" in 10% ballistic gel. That makes it a great self defense round.
However, it's also lower recoil compared to factory ammo using the same bullet, and that makes it a much more enjoyable range round, and one that is still very accurate as the XTPs have an excellent reputation for accuracy. In addition. Midway is currently selling 125 gr XTPs for $15.99 per box of 100. 9 grains of Unique costs me $0.03 and a primer costs me another $0.03, for a total of $0.22 per round, or $11.00 per box of 50. That makes it a very affordable range round that still costs less than the cheapest 38 Special I can find, and way cheaper than the cheapest .357 Mag I can find. (Tula .38 Special in their 130 gr FMJ loading is $11.50 per box, and Tula 158 gr FMJ is $13.95 per box.)
So in short, I don't have "self defense" ammo, I have an inexpensive JHP range round that I happen to carry in my self defense revolver. And since I load a lot of it and regularly expend in on the target range, it's actually the truth.