Well, you don't show your original XML format.
Why did you comment out that Get-Content? it will not work without it.
So, if we take the below example, it works as expected.
# Simple XML version
$SimpleXml = $null
$SimpleXml = @"
<?xml version="1.0" encoding="utf-8" ?>
<configuration>
<name>Apple</name>
<size>1234</size>
</configuration>
"@
# New node code
[xml]$XmlDoc = Get-Content -Path variable:\SimpleXml
$runtime = $XmlDoc.CreateNode("element","runtime","")
$generated = $XmlDoc.CreateNode("element","generatePublisherEvidence","")
$generated.SetAttribute("enabled","false")
$runtime.AppendChild($generated)
$XmlDoc.configuration.AppendChild($runtime)
$XmlDoc.save("$pwd\SimpleXml.xml")
Get-Content -Path "$pwd\SimpleXml.xml"
# Which creates this:
<?xml version="1.0" encoding="utf-8"?>
<configuration>
<name>Apple</name>
<size>1234</size>
<runtime>
<generatePublisherEvidence enabled="false" />
</runtime>
</configuration>
Also Write-Host is never needed unless you are coloring screen output.
Write-Output is the default and automatically write to the screen, whether you specify Write-Output or not.
So, all of these to the same thing - output to the screen.
$SomeString = 'hello'
Write-Host $SomeString
Write-Output $SomeString
'hello'
"hello"
$SomeString
"$SomeString"
($SomeString)
("$SomeString")
$($SomeString)
# Results
hello
hello
hello
hello
hello
hello
hello
… yet, it's your choice.