Hi Jay,
That doc page does say that the filter can can accept either a vector or a matrix. But we have to look at how the data in the input is interpreted.
Sample- and Frame-Based Concepts states that "in the MATLAB environment, System objects always process frames." That page goes on to explain "the block interprets an M-by-1 vector as a single-channel signal containing M samples per frame. Similarly, the block interprets an M-by-N matrix as a multichannel signal with N independent channels and M samples per channel." Even though that statement is given in the context of Simulink blocks, I think it also applies to system objects. So the input of a 1 x 2^16 row vector is interpreted as one sample in time of each of 2^16 independent channels, as opposed to 2^16 time samples of one channel. See also Create Signals for Frame-Based Processing