In PD you can only store one value per x step. That means you can not make a sequencer that uses polyphony. In real world, arrays are used to store multiple values and can have even 3 or more dimentions, values could be stored on any point without one affecting another.

Are there any alternatives to this in Pure Data? Currently I assume it is only possible to do this by writing an external file/list, like xml, but that really isn't the most efficient solution.

Is it possible to actually store real value on any coordinate in array, like [x2 y10 23]?

[iemmatrix/matrix] ?

you can implement multidimensional arrays it by hand, by having every "dimension" be a multiple of the other dimensions. so if you have for instance a 2X3X4 matrix you would have 24 entries. index into the array by multiplying by the lower dimensions: to get to the first index multiply by 12 (so for instance index 1 of the first dimension actually starts at position 12 in the array), then multiply the second index by 4 and add it to the first, and finally add the final index with no multiplication.
this is actually the way multidimensional matrices are implemented in c
... or use iemmatrix