You are diffing all files from dir1 with all files from dir2. If you only want to diff file1 vs. file1, etc. (UNTESTED):

use strict;
use warnings;
use File::Basename;

my @tst1 = qw(
    /dir1/file1
    /dir1/file2
    /dir1/file3
);

my @tst2 = qw(
    /dir2/file1
    /dir2/file2
    /dir2/file3
);

chomp @tst1;
chomp @tst2;

for my $t1 (@tst1) {
    for my $t2 (@tst2) {
        next unless basename($t1) eq basename($t2);
        my $status = system "diff $t1 $t2 > /dev/null";
        print "$status\n";
    }
}
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