I'm lost. Why is "pepper" not found in your desired output, and how does "sugar" find its way into your desired output when it's not part of your input files?

use 5.010;
use strict;
use File::Temp ();
use Path::Class ();

my $temp  = Path::Class::Dir->new( File::Temp::tempdir() );
my $file1 = $temp->file('file1.txt');
my $file2 = $temp->file('file2.txt');

# Create files to operate on.
# You already have these files, so you don't need to make them.
print { $file1->openw } <<DATA;
pizza
pickle
omellete
coke
blackforest
croissant
DATA

# (note: following includes tabs - beware if
# copying and pasting from PerlMonks!)
print { $file2->openw } <<DATA;
salt    pizza    1
salt    pickle    1
pepper    omelette    1
pepper    pickle    1
sugar    coke    1
DATA

# OK, now let's start the real work...

# List of all meals
my @meals = $file1->slurp(chomp => 1);

# This will help us generate a list of all ingredients.
my %ingredients;

# Record pairings between ingredients and meals
my %pairings;

# Loop through file2 building up previous hashes.
for ($file2->slurp(chomp => 1))
{
    my ($ing, $meal, $bool) = split /\t/;
    
    $ingredients{$ing}     = 1;     # record that the ingredient exist
+s at all
    $pairings{$ing, $meal} = $bool; # record the pairing of ingredient
+ and meal
}

# List of all ingredients
my @ingredients = keys %ingredients;

# For each pair of ingredient and meal...
for my $i (sort @ingredients)
{
    for my $m (sort @meals)
    {
        printf(
            "%s\t%s\t%d\n",  # format string
            $i,  # ingredient
            $m,  # meal
            $pairings{$i, $m},  # paired?
        );
        # Note that $pairings{$i, $m} is
        # converted to an integer by printf
        # because of the '%d' formatting
        # code. Thus if there's no pairing,
        # we get '0'.
    }
}

# Clean up temp dir
$temp->rmtree;
[download]

An alternative way of writing the output loop would be to use List::MapMulti, in which case it would be:

my $pairs = iterator_multi(\@ingredients, \@meals);
while (my ($i, $m) = $pairs->())
{
    printf("%s\t%s\t%d\n", $i, $m, !!$pairings{$i, $m});
}
[download]

Or even:

say for mapm { join "\t", @_, 0+ $pairings{$_[0], $_[1]} } \@ingredien
+ts, \@meals;
[download]

One more point about the OPed code: variable names like  $1file and  $2file are tres illegal: a user-code defined variable name must begin with an alpha. (Perl defines special variables like  $1 $@ $^W etc., but we all know that Perl is special!) (Actually, I believe there is a way around the alpha-first-character rule for user code, but that's another story.)