I think your sample code is great in that it shows just how well the variable $. works when used correctly (in that if you are working with two filehandles, it really does work just like a pronoun by referring only to the most recently handled file).

But I don't think $. is fancy code, any more than I think using

sub my_func {
   my $arg1 = shift;
   my $arg2 = shift;
   ...
}
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is fancy code for using an implied $_ in the argument assignements. $. is there so I, as a programmer, don't have to add code (and potentially bugs) to the process of counting which line I am on in a file, and as such it may help to make programs work better. I would say that using $. more than a couple of lines away from the filehandle is a bad idea-- same rules as for pronouns in spoken language.