I'm not sure if this is a bug. Perhaps you haven't completed this feature, or perhaps it's really a bug, or maybe you don't want this feature/publish this feature for players and data pack creators.
Structure files have palettes. The only structure files that use multiple palettes are shipwrecks. Several palettes allow automatic selection of a set of blocks for a structure, so that one structure can have several variations of the same block shape. By default, each structure has one palette.
The problem is that it is not possible to create a structure with multiple palettes in the game and the only way to do this is to edit the structure file manually. It seems like this has always been the case since the introduction of palettes.
But I noticed that the save functionality still exists, but it seems (I'm not sure) to be disabled. In StructureTemplate::fillFromWorld you need to remove 1 line of code: this.palettes.clear(), and then saving the same structure of the same shape but with different blocks will create a new additional palette.
I'm not sure this will work perfectly and I'm not sure if this is how you intended this feature.
Edit: Yes, it doesn't work perfectly. I changed the shape of the structure and saved it again, but instead of overriding the structure I got a new palette, so I conclude that this is not really a bug.
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I'm still not sure as the developers have only recently started documenting some technical changes to the game, so I'd like to keep this issue open until the developers themselves respond
Closing this bug report based on your edit, concluding yourself that this is not a bug.