It is protected from modification because in applicationHost.config file you'll find this:
<requestFiltering>
<fileExtensions allowUnlisted="true" applyToWebDAV="true">
<add fileExtension=".asa" allowed="false" />
<add fileExtension=".asax" allowed="false" />
<add fileExtension=".ascx" allowed="false" />
<add fileExtension=".master" allowed="false" />
<add fileExtension=".skin" allowed="false" />
<add fileExtension=".browser" allowed="false" />
<add fileExtension=".sitemap" allowed="false" />
<add fileExtension=".config" allowed="false" />
<add fileExtension=".cs" allowed="false" />
<add fileExtension=".csproj" allowed="false" />
<add fileExtension=".vb" allowed="false" />
<add fileExtension=".vbproj" allowed="false" />
<add fileExtension=".webinfo" allowed="false" />
<add fileExtension=".licx" allowed="false" />
<add fileExtension=".resx" allowed="false" />
<add fileExtension=".resources" allowed="false" />
<add fileExtension=".mdb" allowed="false" />
<add fileExtension=".vjsproj" allowed="false" />
<add fileExtension=".java" allowed="false" />
<add fileExtension=".jsl" allowed="false" />
<add fileExtension=".ldb" allowed="false" />
<add fileExtension=".dsdgm" allowed="false" />
<add fileExtension=".ssdgm" allowed="false" />
<add fileExtension=".lsad" allowed="false" />
<add fileExtension=".ssmap" allowed="false" />
<add fileExtension=".cd" allowed="false" />
<add fileExtension=".dsprototype" allowed="false" />
<add fileExtension=".lsaprototype" allowed="false" />
<add fileExtension=".sdm" allowed="false" />
<add fileExtension=".sdmDocument" allowed="false" />
<add fileExtension=".mdf" allowed="false" />
<add fileExtension=".ldf" allowed="false" />
<add fileExtension=".ad" allowed="false" />
<add fileExtension=".dd" allowed="false" />
<add fileExtension=".ldd" allowed="false" />
<add fileExtension=".sd" allowed="false" />
<add fileExtension=".adprototype" allowed="false" />
<add fileExtension=".lddprototype" allowed="false" />
<add fileExtension=".exclude" allowed="false" />
<add fileExtension=".refresh" allowed="false" />
<add fileExtension=".compiled" allowed="false" />
<add fileExtension=".msgx" allowed="false" />
<add fileExtension=".vsdisco" allowed="false" />
</fileExtensions>
<verbs allowUnlisted="true" applyToWebDAV="true" />
<hiddenSegments applyToWebDAV="true">
<add segment="web.config" />
<add segment="bin" />
<add segment="App_code" />
<add segment="App_GlobalResources" />
<add segment="App_LocalResources" />
<add segment="App_WebReferences" />
<add segment="App_Data" />
<add segment="App_Browsers" />
</hiddenSegments>
</requestFiltering>
I was thinking of changing the applicationHost.config file because of this, but in fact we're making it too complicated: since we have a WebDAV mapped drive/folder, you can open your website directly from that folder and edit it in-place. No need to publish anymore.
If you still want to work locally, then publish to the WebDAV drive, you can instead use the Copy Website command instead of the Publish Website command.