When a flower or other plant is placed on a block, the plant is not placed in the middle of the block, but is offset from the middle of the block by some random amount in x and z.

These offsets are always the same, for the same block coordinates. Only the x and z coordinates matter. If blocks have different y coordinates, flowers on them will line up perfectly.

Even for worlds with different seeds, if the coordinates are the same, plants will always be offset by the same amount. This is a similar mechanic as the placement of bedrock blocks, which are also in the same place regardless of world seed.