sorry, resending without html encoding
I just tried doing the same thing with xmlfile (what is the difference
between the two?) as below: 
<util:XmlFile Id="ConfigDNSPath"
        File="[#Fi.config]"
        Sequence="1"
        Action="createElement"
        Name="Plugin.Dns.Properties.Settings"
        ElementPath="configuration/applicationSettings" />

<util:XmlFile Id="ConfigDNSDnsServerKey"
        File="[#Fi.config]"
        Sequence="2"
        Action="createElement"
        Name="setting"

ElementPath="configuration/applicationSettings/Plugin.Dns.Properties.Settings"
/>

<util:XmlFile Id="ConfigDNSDnsServerKeyName"
        File="[#Fi.config]"
        Action="setValue"
        Sequence="3"
        Name="name"
        Value="DNSServer"

ElementPath="configuration/applicationSettings/Plugin.Dns.Properties.Settings/setting"
/>

<util:XmlFile Id="ConfigDNSDnsServerKeySerialize"
        File="[#Fi.config]"
        Action="setValue"
        Sequence="3"
        Name="serializeAs"
        Value="String"

ElementPath="configuration/applicationSettings/Plugin.Dns.Properties.Settings/setting[...@name='DNSServer'[\]]"
/>

<util:XmlFile Id="ConfigDNSDnsServerValue"
        File="[#Fi.config]"
        Sequence="4"
        Action="createElement"
        Name="value"

ElementPath="configuration/applicationSettings/Plugin.Dns.Properties.Settings/setting[...@name='DNSServer'[\]]"
/>

<util:XmlFile Id="XML.Plugin.Config.DNS.DNSServer"
        File="[#Fi.config]"
        Sequence="5"
        Action="setValue"
        Value="[CRM.PLUGIN.CONFIG.DNS.DNS_SERVER]"

ElementPath="configuration/applicationSettings/Plugin.Dns.Properties.Settings/setting[...@name='DNSServer'[\]]/value"
/>


with a config file that started out like this:  
<applicationSettings>
        <Plugin.Dns.Properties.Settings>
        
        </Plugin.Dns.Properties.Settings>
</applicationSettings>


and resulted in this (notice the extra empty elements):
<applicationSettings>
        <Pareto.Crm.Admin.Plugin.Dns.Properties.Settings>
                <setting name="DNSServer" serializeAs="String">
                        <value></value>
                </setting>
                <setting/>
        </Pareto.Crm.Admin.Plugin.Dns.Properties.Settings>
        <Pareto.Crm.Admin.Plugin.Dns.Properties.Settings/>
</applicationSettings>

Can XmlFile not do updates?
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