I hope you like these ideas, I'm sure they are not totally novel.
I found it silly to have stones sit in neat rows in a pile: they should be a rough heap.
The dump heap 'cheat' is equally silly, but in the oposite extreme: such a large number of big boulders should spill and be in the way.
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1) Landfill.
Have stone stacking (ex: in a dump-zone) consolidate into a solid heap of agregate when more than seven are on the tile.
The rocks lose their individual qualities, and lots of rock is lost forever, but it does provide a new means to create artificial landscape besides construction.
(Other dumped stuff that happens to be in the same tile will likely be lost as well...not living creatures surely)
It would be like non-arable soil for engraving purposes.
Maybe add spontaneous spilling over to adjacent tiles to form 'ramps' before being consolidated.
This thought led me to this next suggestion:
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2)stockpile 'spillage heap' option (stacking):
Have rocks and other 'big-stuff' take up space in a tile,
...have 7/7 bigthings in a tile and it is impassable,
but walkable the next level up.
(Different from the previous suggestion, the items in the heap remain seperate items.)
Stockpile tiles can contain 0-4 pieces of 'bigstuff'.
When all adjacent tiles of a single tile have reached level 4/7, it can now contail 7/7.
A stack of 0-4 stuff counts as a ramp, a 4+ stuff tile counts as impassable on ground level, but creates a virtual floor one level up.
Other neighboring non-stockpile, impassable and solid tiles count as being 4+ for this purpose.
Result: stockpiles can now countain lots more crap, but crap becomes increasingly difficult to retrieve as it gets burried in more crap.
It also becomes an impediment to traffic if badly planned.
movement hazard! Heaps should be difficult to traverse, causing dwarves to stumble and fall.