The advantage is that it is more consistent and intuitive for people using it in the future.
I was going to suggest that bee nests do save their block state, but I remembered that they save block data and not block state.
The bug is that the game still states the structure was generated despite no blocks being replaced/placed.
It should state "Failed to generate structure" if it is intended for mesa mineshafts to only be generatable in badlands.
(In my opinion it should be generatable in any biome, but I understand if that counts as a feature request.)
Can confirm in 1.19 Pre-Release 1