Quote:
    push(@{$category}, $item) if (@{$category});
...
    Note that this version would only push items with pre-declared categories, the rest would be silently discarded

I'm afraid that version will silently discard everything. @{$category} will never be true, because all of your pre-declared arrays start with zero elements.

You could do something like this:

@fruit = (undef);
@meat  = (undef);
@dairy = (undef);

while (<FOOD>) {
  chomp;
  ($category, $item) = split(' ', $_);
  push(@{$category}, $item) if (defined @{$category});
}

shift @fruit;
shift @meat;
shift @dairy;
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But really, why would you want to? I think it's much simpler to restrict the categories if you use a hash of lists.