XML declaration being removed while using Element Tree in Python. Just need to add version parameter <?xml version='1.0'?>

Because that is a bit of a sophisticated rendering beyond elementTree, consider XSLT, the special-purpose language designed to transform XML files. Python can run XSLT 1.0 scripts with third-party module, lxml, or via command line to an external .exe like Unix's (Mac/Linux) xsltproc.

Specifically, the below XSLT script runs the Identity Transform to copy document as is and removes encoding from header declaration and retains version.

XSLT (save as .xsl file, a special .xml file)

<?xml version="1.0" encoding="UTF-8" ?>
<xsl:stylesheet version="1.0" xmlns:xsl="http://www.w3.org/1999/XSL/Transform">
    <xsl:output method="xml" indent="yes" omit-xml-declaration="yes"/>

      <xsl:template match="@*|node()">
        <xsl:copy>
          <xsl:apply-templates select="@*|node()"/>
        </xsl:copy>
      </xsl:template>

    <xsl:template match="/">
        <xsl:text disable-output-escaping="yes"><![CDATA[<?xml version="1.0"?>]]>&#xa;</xsl:text>
          <xsl:apply-templates select="@*|node()"/>
    </xsl:template>

</xsl:stylesheet>

Python (using lxml)

import lxml.etree as et

... 
# LOAD XSL
xsl = et.parse('xslt_script.xsl')

# TRANSFORM ORIGINAL tree
transform = et.XSLT(xsl)
result = transform(tree)

# PRINT RESULT TO SCREEN
print(result)

# OUTPUT RESULT TO FILE
with open('output.xml', 'wb') as f:
    f.write(result)

Python (using command line to xsltproc)

from subprocess import Popen

...
tree.write("file.xml", xml_declaration=True)

proc = Popen(['xsltproc -o output.xml xslt_script.xsl file.xml'], 
             shell=True, cwd='/path/to/working/directory',
             stdin=None, stdout=None, stderr=None)