Absolutely safe. The purpose of that (that's called a "cannelure", by the way) is to give a little lip inside the case for the bullet to sit on. As you may or may not know, the 45 Colt was originally a "black powder" cartridge, and the case was filled full of powder. The bullet sat atop the powder. With smokeless powder cartridges, they use MUCH less powder (my loads use 8 grain of Unique, versus the 40 grains of black that was the original load) and there is a large air space between the bullet and the powder, so the little inside lip for the bullet to sit on.
This lip is not necessary, and many manufacturers don't use it. But some do. It does not hurt anything. It does not weaken the brass. Probably by the second firing the cannelure will have fireformed out.