I am not sure if this is a problem in pkgchk or the underlying configuration APIs
that it uses, but if I add the following ProtocolHandler.xcu file to a UNO package:

<?xml version="1.0" encoding="UTF-8"?>
<oor:node xmlns:oor="http://openoffice.org/2001/registry"
xmlns:xs="http://www.w3.org/2001/XMLSchema" oor:name="ProtocolHandler"
oor:package="org.openoffice.Office">
 <node oor:name="HandlerSet">
  <node oor:name="com.sun.star.comp.ScriptProtocolHandler" oor:op="replace">
   <prop oor:name="Protocols">
    <value>script:*</value>
   </prop>
  </node>
 </node>
</oor:node>

and then install the package using pkgchk the file ends up in
<installdir>/user/uno_packages/cache/registry/data/org/openoffice/Office
but the line:

<prop oor:name="Protocols">

has changed to:

<prop oor:name="Protocols" oor:type="xs:string">
This causes the settings in the file to be ignored. The type value should not be
added.