If you have MATLAB R2016b or above, BSXFUN was replaced by automatic expansion and you can do it as follows:
>> D = repmat( A, 3, 1 ) - A(:)
D =
0 1 2
0 1 -2
0 4 6
-1 0 1
-1 0 -3
-4 0 2
-2 -1 0
2 3 0
-6 -2 0
otherwise, almost the same as your first solution:
>> D = bsxfun( @minus, repmat( A, 3, 1 ), A(:) ) ;
Both are based on the fact that indexing A linearly will read it column first:
>> A(:)
ans =
1
3
1
2
4
5
3
1
7
