Depends on what I'm doing. Nine times out of ten if I'm fighting I am not going to keep my shoulders in line with the hips. For power and throw resistence that's a disaster and sure to lead to too much foot work or muscle use. But many times at the completion / follow through of a throw they meet or line up. But the follow through or completion is when it's all over. It's what precedes that -that is the real jewel of the martial arts-preventing unbalancing and fit-ins and strikes or kicks. and all of those are best done without the hips and shoulder in line IMO...YMMV.
The real million dollar question is WHHHHYYYY we turn the waist and what affect that HAS on the hips. Hell even that isn't accurate either. Its more like what is the waist drawing on...through the hips.
Example: most anyone who isn't a blithering idiot knows how much trouble you get into in firing the shoulders- if you are trying for internal power right?
IMHO the hips are the shoulders of the lower body! They prevent / cause just as much -if not more- trouble than all the bad habits in the shoulders.
Dan