You could set xml_declaration argument on write function to False, so output won't have xml declaration with encoding, then just append what header you need manually. Actually if you set your encoding as 'utf-8' (lowercase), xml declaration won't be added too.
import xml.etree.cElementTree as ElementTree
tree = ElementTree.Element('tmx', {'version': '1.4a'})
ElementTree.SubElement(tree, 'header', {'adminlang': 'EN'})
ElementTree.SubElement(tree, 'body')
with open('myfile.tmx', 'wb') as f:
f.write('<?xml version="1.0" encoding="UTF-8" ?><!DOCTYPE tmx SYSTEM "tmx14a.dtd">'.encode('utf8'))
ElementTree.ElementTree(tree).write(f, 'utf-8')
Resulting file (newlines added manually for readability):
<?xml version="1.0" encoding="UTF-8" ?>
<!DOCTYPE tmx SYSTEM "tmx14a.dtd">
<tmx version="1.4a">
<header adminlang="EN" />
<body />
</tmx>
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