The conditional operator (?:) usually makes code less readable, especially when nested.

my %results = map {
   my ($x, $y) = split(/=/, $_, 2);
   if (defined($y) && $y =~ /^#(.*)/) {
      $y = fn($1);
   }
   elsif (!defined($y)) {
      $y = fn($x);
   }
   ($x, $y)
} split(/,/, $string);
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If you wanted terse:

my %results = map {
   /^([^=]*)(?:(=)(#)?(.*))?/s;
   ($1, ($3 ? fn($4) : ($2 ? $4 : fn($1))))
} split(/,/, $string);
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Update: Added terse snippet.