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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