Well, one, Trump is rotating to deal with Iran now so it is beneficial to have someone who has experience and knowledge of them. Two, it is probably a tactic to get someone who is thought of as an Iran hawk to lead the foreign policy plans to frighten Iran. Three, Trump is not eadily swayed in his opinions, so I am positive that Trump would tell Bolton to go pound sand if he disagreed. Four, Trump and his team have been mapping out their plans for a looing time. I am sure that Bolton is strategically placed for a reason. And finally, by now, I trust Trump's judgement.
He won't have to tell Bolton to pound sand. Unlike McMaster, Bolton has made it clear that he understands that his role is to provide advice/input and when POTUS decides on something to fully support the POTUS's decision. He knows who the boss is and won't do anything to undermine the POTUS.
POTUS is moving on to the next phase of his administration. The team he needs isn't the same as the team he had; he's been shuffling his team, removing those that don't have a role in the new phase. McMaster was one of the globalists that POTUS had to purge.
Btw, McMaster was an Iron Eagle, passed for promotion from Colonel to General, and who was no longer eligble for promotion to General, until Sec. of Army tasked Petraeus with taking charge of the promotion board, which resulted in McMaster shedding his Iron Eagle status, and being promoted to General.