Not sure if this is supposed to happen, but when I tried to clone a large area, it said the area was too big, at about 13000 blocks trying to be cloned. I checked on MCedit to see if the number of actual blocks (not air) was that many, but the block count was under 4096, and air was taking up the rest of the space. So, from what I can tell, it included the air blocks in the count, and said it was over the limit.
Here's my exact command:
/clone ~14 ~ ~2 ~-7 ~26 ~-19 ~-40 ~ ~-19 masked
The result:
[11:02:30] Too many blocks in the specified area (13068 > 4096)
MC-50056
In clone masked, air blocks are included
Resolved
Works As Intended
0
That isn't how masked works.
The command checks the entire volume (box) your'e cloning, that is 13000 blocks which is above the 4096 allowed.
IF you have under 4096 total block volume, the command will clone all non-air blocks to the new location.
This was done to prevent lag since the game still has to check all block spaces and see if they need to be cloned or not.