It seems alerts appear in chronological order (latest at the top) by default and you can no longer customize the order in which they appear. Is this the case or am I overlooking the customization settings?
Yup, it seems the choice between chronological and sorting by app is gone and we're left with chronological order only.
I don't mind because when you sorted by app only ten notifications for that app was showed. With chronological the limit is 50 or so. (I didn't count them)
You're not overlooking anything, I couldn't find it either. Hopefully they'll re-add the option to sort by app again because I hate it the way it is now.