Just iterate over the keys of %in to build your new arguments hash:

...
my %in = (
  arg1      => 'foo',
  arg2      => 'bar',
  arg3      => 'baz',
  ignore    => 'this entry',
  idx       => 'index',
  newperiod => "bar",
);

my %xsltargs;
map { $xsltargs{$_} = $in{$_} } 
  grep /^arg|^idx$|^newperiod$/, keys %in;

...

my $results = $stylesheet->transform( $source, 
  XML::LibXSLT::xpath_to_string(%xsltargs) );
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