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while(my $s = <$fh>) {
  $s =~ /^ ?Query/ && $match_count1++;
}

v5.32.1
tempfile.txt is size 29 Mb
0.121957 read lines from disk and do RE (32571 matches).
9.511288 read lines from in-memory file and do RE (32571 matches).

while(my $s = <$fh>) {
  index( $s, 'Query' ) != -1 && $match_count1++;;
}

v5.32.1
tempfile.txt is size 29 Mb
0.092390 read lines from disk and do RE (32571 matches).
0.051797 read lines from in-memory file and do RE (32571 matches).