Sorry this has taken a while to reply to, and thanks for the like.
To answer your question, I think it isn't to much of an issue for the reasons you pointed out. If you are up against only magic users, I suggest the frost atronach, whereas against a wider variety you should use fire ones. Since draugr are resistant to frost, flame atronachs will be preferable 90% of the time.
Sorry this has taken a while to reply to, and thanks for the like.
To answer your question, I think it isn't to much of an issue for the reasons you pointed out. If you are up against only magic users, I suggest the frost atronach, whereas against a wider variety you should use fire ones. Since draugr are resistant to frost, flame atronachs will be preferable 90% of the time.