Where a piece of loot represents a character’s growth and progression, I don’t worry much about where it comes from, and I don’t think the players do either. If a character earns a milestone in the moment (or even between sessions), I am okay with the item just showing up, almost as if the character had it all along. As the DM, I tend to gloss over how these new items show up. Sometimes, the players come up with an awesome explanation of how the items came to be, which is really cool. They know the nuances of their characters infinitely better than I do.
I tend to use the above philosophy and not worry about the fiction too much because I want my players to experience the joy and thrill of “shopping” in the books when they go to pick out milestones, rather than my including too many milestones that exist in the world and forcing my idea of things on players (though a good mix is always fun).