I imagine the animators did a bunch of studies on Hayden's movements while designing Anakin for the Clone Wars. His walk and way of movement would sell the idea that this is Anakin Skywalker. That they kept those movements for Darth Vader in Rebels would be inspired. More inspired would be if Hayden's performance actually did take movement queues from Prowse's work as Darth Vader from time to time, so that when the animators started working on it they were actually getting both actors movements right from the start.
I do recall the behind the scenes featurette for Revenge of the Sith that talked bout the process of recreating Darth Vader's helmet and its fitting to Hayden. At the very end, when you see Hayden in the suit (strapped down to the table), his head movements, intentional or not, were exactly Darth Vader. Like Prowse was in there, but we know it was Hayden.