If you really want to write it that way, I think you'd need to use do {...}, e.g. something like this

my $s = "a,b=c,e=#f";

sub fn { "fn(@_)" }  # dummy function

my %result = map {
        /=#/ ? do { my @l = split(/=#/,$_,2); ( $l[0], fn($l[1]) ) }
             : /=/ ? split(/=/,$_,2)
                   : ($_,fn($_))
    }
    split(/,/, $s);


use Data::Dumper;

print "$s\n";
print Dumper \%result;
[download]

Output:

a,b=c,e=#f

$VAR1 = {
          'e' => 'fn(f)',
          'a' => 'fn(a)',
          'b' => 'c'
        };
[download]