Yes, this has been my experience as well. Whether it be actual burn in of the driver/cable, brain burn in, or some combination of the two, the more I have listened to the atlas the more I have grown to appreciate its sound signature. I have been going back and forth between the atlas and my EE phantom and while the atlas clearly has emphasized bass, there is still a lot of detail and presence to the mids and highs without the bass bleeding in to overpower/interfere with them. Compared to the phantom, the mids have a little less detail and texture, and they are less forward, but in general, I would consider the atlas mids to be well detailed with very good texture, and would not call them recessed. Listening to the atlas, there are some time it feels like you have to aurally peer through (or perhaps peer over) the bass to focus in on the mids and, to a lesser extent, the highs, since the bass is what hits you first; however, once you do focus in on them, you find that there is a lot of detail and texture there that is not crowded out interferes with. The bass serves to ground the sound and round out the bottom of the notes.
I also agree that the bass seems to have have settled and tightened and the mids and highs become more in focus as I have used the atlas (again be it real burn in, me getting used to the sound, or some combination of both).