MATLAB uses column order for historical reasons.
The very early versions of MATLAB were implemented in FORTRAN and were largely based on the LINPACK and EISPACK FORTRAN libraries, which, unlike C, use column order. Although it was (mostly) converted to a C implementation, when it was initially commercialized, it retained the use of column order.
As far as I know, there are no inherent advantages or disadvantages for arrays of columns or rows, it is just a choice to be made anyway.
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