I think it will store ok. The 6 inch curves should nest, the 4 inch curves can nest into each other and fit inside the curve of the 6 inch. With regard to the magnets store the pieces alternating top and bottom... er... I think I said that right. So place six inch tower sides first one up side up, the next one up side down and so on... the magnets are then at least a wall thickness away from each other. Same with the flat walls... I believe the magnets are in the bottom half, so it just means paying a little closer attention when packing up. Maybe use the trick of coloring the top edge one color and the bottom edge another... then you can tell in a hurry if one needs to be flipped.
(Posting here as someone who re-packed a whole bunch of resin Tower bits to entrust unto the delicate, responsible hands of airline baggage carriers.)
Half-tower pieces, whether 6 inch or 4 inch, do not nest much at all.
They are going to be a pain, no doubt about it. Might be best off just storing them as full circles with other stuff in the openings, we shall see.
Quarter-round 6 and 4 inch tower pieces nest just beautifully. No issues at all there.
Walls and wall spacers of course, stack wonderfully.
Very efficient, it's like an IKEA flat pack castle.
Wall platforms with the corbels stack pretty ok, the resin prototypes with the clips glued on were a little delicate but the single-piece ABS plastic ones should stack up just fine.