If you want to aggregate results, you need to specify what you are aggregating by. What are you trying to count? Based on what you've written, I will guess you want to know the number of lines of Boundary.out that match each line of DB.out. You can accomplish this by just moving your counter and print statements outside of the foreach loop:

        my $Count = 0;
        foreach my $line (@file1){
            my ($chr, $start, $stop) = @$line;
            if ($chr eq $Chrom && $start gt $ModStart && $end lt $ModE
+nd){
                $Count++;
            }    
        }
        print ("$Gene\t$Chrom\t$ModStart\t$ModEnd\t$Strand\t$ExonCount
+\t$SizeKB\t$Count\n");
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