It probably depends on the weight and length of the assembly. I used to store mine in a padded case, which seemed to work fine, even for transport to dark sites. I also used to keep my focuser locked in the "focused" position for that train. Sure it might need a little adjustment but it worked pretty well.
As to your Flat statement, it really depends on your camera imho. A camera like an ASI1600mm-c doesn't really need flats, if your optics and camera sensor are clean. Other cameras can need flats.
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