I think that I'd transform the string before splitting it:

#! >perl -slw
use strict;
use Data::Dumper;

$_ = 'a,b=c,e=#f';

s[(\w+)=#(\w+)][$1=>fn($2)]g;
s[(\w+)=(\w+)][$1=>$2]g;
s[(?<!=>)(\w+),][$1=>fn($1),]g;

my %results = split ',|=>';
print Dumper \%results;

__END__
C:\test>junk8
$VAR1 = {
          'e' => 'fn(f)',
          'a' => 'fn(a)',
          'b' => 'c'
        };
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