Hmm. That's true. I'm not sure how much this is actually a dichotomy in practice, as opposed to a gradient where some sidekicks are more assistant-like, some are in the middle, and some are more second-in-command like. I'm also not sure to what degree the same people are attracted to both second-in-command and assistant roles, and whether it's for the same reasons. That would affect whether it makes sense to classify them together for this purpose. I can come up with imaginary characters who would only be interested in second-in-command, or only in assistant roles, but they both appeal to me for many of the same reasons.

I kind of feel like it has to do with the sidekick's competence and also the scale of the project. If the project is of a scale where it's possible for the hero to make most of the decisions, and the sidekick is new to it and finds assistant-work hard enough, it'll tend towards that role. If the sidekick and hero keep working together, as they both learn and grow, the hero will want to move on to larger-scale projects, and at some point there will be too many high-level decisions for the hero to make all of them, and at this point the sidekick will have been working with them for a long time and learned a lot, and it seems like it might naturally turn into a second-in-command role. But this would only happen in a situation where roles are fluid; if it were a standard case of a CEO and their executive assistant, the role would be unlikely to change that much. (Although EAs do have quite a lot of decision-making power.)