Let me see how much I misunderstand the "less magical" code:

rename($html_file, "$html_file.bak")    or die;
Makes a copy of the file with the .bak extension

open(my $fh_in,  '<', "$html_file.bak") or die;
Opens the copy of the file for reading

open(my $fh_out, '>', $html_file) or die;
Opens the original file for writing, wiping out the contents?

    while (<$fh_in>) {
while there are file contents in the backup file, do something with them

      # Keep (possibly edited) line
      print $fh_in $_;
   }
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Print whatever the backup file is back into the backup file?

Ok, yeah, I still don't get this. I know I should, I've read enough examples, but I don't.
I read it as making a copy of the file I want to change, wiping out the contents of the original, modifying the copied file somehow and writing the modified text back into the copied file? Why am I not seeing this still?

Also, I don't get the while(<$fh_in>) { s/// } instead of using

my @lines = <$fh_in>;

    for (@lines) { s/// }
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because do I want to do the s/// on the entire file at once? Don't I want to go line by line?

As for the using Perl to write PHP, as ignorant as I may seem about Perl, I am continuously frustrated with moving into PHP. What I find is that the things that PHP does easier than Perl does not outweight the things that I could do easily in Perl that cannot do easily in PHP.