Now this returns me (in a mod_perl environment) formatted text. Can I get rid of this?

Are you surprised this includes white-space?

my $foo = "1. Blah
               2. Blubb
               3. more blah";
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use Data::Dump; dd $foo;
__END__
"1. Blah\n               2. Blubb\n               3. more blah"
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That is how strings work :) See perlintro

And why don't the following work?

A couple of reasons, do this instead

$Workflow[$i]{Body} =~  s/^\s+//mg; # g means global
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