In my in-dev game, Quest For Chevar, I handle this by making downtime the only way to do certain important things, and is automatically a part of getting all your resources back. Downtime is very important, because it’s the only time you can manage relationships with contacts and such, deal with certain kinds of complications that arise during a job, build complex things, do deep research on a creature or organization or the like, and train new features like traits and levels.
It also takes downtime to recover from trauma, regain all spent resources, etc, referred to as an extended rest.
Because of all this, it’s fine to let someone take a downtime endeavor to learn a new skill.