When using the Select Same Tile tool on empty tiles, it only selects empty tiles in chunks that have at least one non-empty tile in them, and ignores empty chunks. Presumably this is due to an optimization to avoid checking tiles in empty chunks, but it causes incorrect results when empty tiles are what you want.
For example, here’s an attempt to select empty tiles in a mostly empty layer on a map with 16x16 chunks:
For what it’s worth though, I haven’t run into actual problems relating to this, it’s just been a curiosity. If it would be a hassle to fix, leave it as-is xP