Some of the .45 acp NT brass uses small pistol primers and some doesn't. It depends on the company, and when it was manufactured. The transition to Non-Toxic primers has been a learning curve for the companies. They first started out using large pistol primers, but couldn't keep them in the pockets. They next tried crimping them, but that wasn't entirely satisfactory, either. The next change was enlarging the flashhole to a larger diameter. This helped quite a bit.
In the process of all this, they found that it wasn't necessary to use large pistol primers at all, so some of the companies have switched to small pistol primers for the NT primers. Whether this is the final iteration or not is yet to be seen.
The Coast Guard is currently shooting Winchester NT primed .40 S&W ammunition in their Sig handguns, with what are supposed to be frangible bullets. In that brass, with that load, the primers are almost flowing out of the primer pockets. It looks like a dangerous overload when you look at only the primers, but measurement of the cases at the juncture of the case wall and web don't indicate excessive pressures. Non-Toxic primers just work differently that what we're used to dealing with.
Back to your original question on how to remove the crimp, there are several means to do that. I use the RCBS primer pocket swaging tool that mounts on a single stage press. Dillon also makes an excellent primer pocket swaging tool, which is bench mounted and dedicated to just that one purpose.
Some people use a deburring tool and remove the crimp by bevelling the mouth of the primer pocket. This works, too, but I prefer to not remove metal. That's just my preference, but I have used this method.
Hope this helps.
Fred