Ahoy matey!
To quote; This might help you understand the teams' thoughts on the matter.
Milestones are not awarded for deeds you have already completed primarily because Milestones are designed to be a progression system for Captaincy specifically – they are for actions you have completed whilst aboard a Captained Ship, much like Pirate Legend commendations that require you to be a Pirate Legend to unlock them.
In addition to this, the team have been hard at work implementing a huge number of stats behind the scenes – which has been a significant undertaking – in order to correctly track and award all of these Milestones for you, your crew and your Ships. We have not had the ability to track many of these actions until now, and so it would have been impossible to retroactively award everything. The most consistent and fairest approach was for all Milestones to be non-retroactive.
When we were originally considering the system, we did discuss and carefully consider this limitation of not being able to award retroactively but ultimately felt that the introduction of Milestones still has a hugely positive impact that makes the Sea of Thieves session more rewarding over the long term, especially as we're rewarding core content that will always be part of the experience.
The rewards for engaging with Milestones are spread throughout the Milestone and overall Alignment Progression. For example, the lowest tier Trophy is available at a lower class level, with upgraded Frames, Bases or Plaques for the same trophy being available for those who heavily invest in a particular milestone. This is intended to reward and represent the players who want more long-term goals and rewards.
There are many rewards unlocked on the overall Alignment Class, which means you can pick and choose which Milestones you want to progress within that Alignment to unlock the reward.
The team had multiple design conversations regarding this and ultimately this will not be changing.
Dropping anchor here.