As long as the file name remains the same and the PI is the enclosing document remains intact and in the same place, you can certainly process the generated XML chunks in any way you want.
I certainly see a usage for these tools to extract a few small parts of a huge document, transform those and then put back the transformed documents in the original document. Note though that in this case you are just doing what XML::Twig already does normally when using the twig_roots/twig_print_outside_roots options (see Building_an_XML_filter for example).
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