Both the CSV export and the CSV tile layer format options keep all rows and columns of empty tiles, so this problem almost certainly stems from your parser or renderer.
Do these layers actually have those empty cells in them, or are they offset? Offsetting layers is merely cosmetic and does not insert new rows/columns into them.
No, I mean offsetting them using the layer Offset properties, or the Offset Layers tool.
Would you mind uploading an example map (TMX) that exhibits this issue when you export as CSV? I want to see if there’s anything odd about the map, or if your CSV plugin is somehow behaving differently from mine.