How to reproduce:
1.run:/place structure minecraft:desert_pyramid 46 -25 39 in superflat world
2.Note the center of pyramid is 46 -64 39(bedrock),not 46 -25 39
Linked issues
duplicates 1
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related to MC-251332
It's actually the same issue. Resolving as a duplicate of MC-251332.
This structure is programmed to set itself on the ground, like most above-ground structures. /place abides to the generation rules, except conditions.