You seem to be confused about vocabulary. \@numbers takes a reference to @numbers, which is the opposite of “dereferencing“.
It is needed because the natural representation for a matrix is an array of arrays. Since a perl array can only hold scalar values, arrays of arrays are actually arrays of references to arrays. PerlLoL goes into a lot more detail about this concept.
Without the backslash, all numbers would be squashed together inside @matrix without structure. The result would effectively be a list, not a matrix.
The question about split is easy to answer by looking at the doc. Without any argument, split splits $_ on whitespace. It is equivalent to split /\s+/, except that leading whitespace in $_ is ignored.
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