I read again and again that the first 3 episodes of this show (2 of which are without Tempest), are NOT a "pilot" because British TV didn't do that. But this show was made with an American audience in mind and American TV Networks wanted pilots.
After episode 3, there is a definite change in the show. Opening music, part of the cast is gone, Beamish goes from an enthusiastic, green but capable Lieutenant to Hudson Lowe. (He also goes from Christopher to Edward.) Last episode it's September and now it's May. Dan suddenly has a strikingly new crew minus a few trouble makers who show up later as Bad Buys (notably Capt Jack Rackem)
Woodes Rogers (Alec Clunes) suddenly disappears. (along with the capable Andrew Crawford) Oh, we're told he sails off to rejoin the Royal Navy and fight the new War with Spain (this week) but I get the very strong feeling he wasn't written out as he is in fact "suddenly" gone at the opening of episode 4. We don't see him leave, we're only told. He's merely mentioned as having shipped out that morning and Dan Tempest is surprised. He had no clue a ship was fitting out to leave? That Beamish is now in charge?
This didn't happen overnight. But in the series it does. And the tone of the show subtly changes. This is where I read of all the noise about it not being a pilot, Clunes left the show, Clunes was only signed for 3 episodes. They wrote and filmed around Shaw who couldn't be there for the first 2 episodes. We'll never know. I can almost wish it had kept on with Clunes - he was the best actor in the production. Beamish as his right-hand man, competent instead of dense. Tempest butting heads with Rogers would have been outstanding.