I would never book flight or hotel through 3rd party portal unless there's a substantial discount. Booking direct work better 90% of the time.
Many aggregators offer big discounts for minor things like logging in or signing up for a newsletter.
$400 off for logging in - sure!
I think they have contracts in place about pricing for non-logged in users (ie. Neither of us will undercut the other). But when you're a customer, they suddenly offer much better deals. Yes I will take the 'loyalty bonus' of free extra 5 days stay for booking a weekend - thanks!
Some of the aggregators are so desperate to get customers that they will give you something for $0. I rented a car for a week for $0 through easyrentcars because I signed up through a refer link for example.