KeyAttr should be 'id', (which is set by default anyway), you also need to set on ForceArray (a single 'tc' element would parse differently otherwise, have a look in the docs.)

The total code is then as simple as...

my $xml_string = qq|
<exec>
    <tc id="001.001" version=""/>
</exec>|;

my $xml_simple = XMLin( $xml_string, 'ForceArray' => 1);

$xml_simple->{'tc'}->{'001.001'}->{'version'} = "new value";

print XMLout($xml_simple);
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