I think Jorgen's idea raises a good point, because as it stands currently this system will be tricky if it only matches ranks and not required skills.
I am thinking particularly of the naval admin commands, actually. If I have a hierarchy that requires 15 admirals of various levels, the proposed changes will ensure that I have 15 admirals of the appropriate levels available to fill those ranks. However there is no guarantee that I will have enough admirals with, e.g., Mining or Terraforming skills to command my Mining or Terraforming admins. So we end up with a situation where leaders are promoted to admiral ranks but don't have any job as they do not fit the auto-assignment criteria.
With the present system, although it is some micro-management I simply expand my admin hierarchy as I receive new admirals and adapt my hierarchy over time based on what personnel I have, or in some cases may leave a command empty until a qualified leader is promoted. To me it is interesting to tend this system over time and see it evolve organically and I have said as much on the subject but I understand that most people dislike the micromanagement involved.
With an auto-promotion system, I will only see new admirals if I create jobs for them or manually promote them, which is probably more realistic but is also problematic if those jobs won't actually be filled. At the same time, I don't want a system that promotes only a "qualified" leader for any unfilled command as then the officer system ceases to be interesting IMO; in real life the person who gets promoted is often not the person who should be promoted (which we have an option to simulate further with the Political skill, but even promoting the "right man for the wrong job" can happen), so why should Aurora be different? It is not unrealistic for a skilled battlefleet captain to be promoted to admiral and stuck into a Mining or Terraforming command which she is unsuited for, and I think it makes sense to allow for this to happen as long as there is some mechanic that this person will not just be a warm body in a chair (which might be realistic - but maybe too much so!
).
Thus I prefer Jorgen's idea that even someone completely unqualified will get a job and develop the appropriate skills at a higher rate, honestly this makes sense anyways as learning by doing is a quite typical process in any field (although some people always will refuse to learn from their experiences...) and I'm unsure why it isn't already how things work at least for specialized commands. For admin commands as well as the specialized sub-command modules I think this makes sense; maybe for the generalized ship commands it is not necessary though, since these jobs have such broad responsibilities that the current system is probably fine in those cases.