If I want a tight, focused, new type sound, yes I'll time align all tracks to the snare, even toms/kick. Subtle, I know, but over all the tracks it adds up.
If I want a vintage, live, natural, indie type sound, I will not change any time delay. Except possibly the under-snare mic if there is one.
I have found that time aligning can really help the sound of a kit in a lot of cases too.
I too reference to (an) overhead, which ever one's snare hit happens latest in time. Or actually I'll choose what ever is the latest track, but it's always an overhead since they are the farthest away. That way I have to slide the waves to the right, instead of having to delete time from the beginning of the waves and slide them left.
What you use as reference is actually all relative. What you have to do is decide what you want the main focus of your kit to be. And align all (or just the overheads) to that.