Instead of having a separate OpenSearch description file and then the results in Atom, why not put the OpenSearch description in the Atom header, eg instead of:
<OpenSearchDescription>
<ShortName>HubLog</ShortName>
<Description>weblog</Description>
<Contact>alf@hubmed.org</Contact>
<Url type="application/atom+xml" template="http://hublog.hubmed.org/cgi-bin/mt/mt-search.cgi?IncludeBlogs=2&search={searchTerms}&Template=opensearch"/>
<Url type="text/html" template="http://hublog.hubmed.org/cgi-bin/mt/mt-search.cgi?IncludeBlogs=2&search={searchTerms}"/>
<LongName>HubLog</LongName>
<Image height="16" width="16" type="image/vnd.microsoft.icon">http://hublog.hubmed.org/favicon.ico</Image>
</OpenSearchDescription>
have
<feed xmlns="http://www.w3.org/2005/Atom" xmlns:opensearch="http://a9.com/-/spec/opensearch/1.1/">
<title>HubLog</title>
<id>tag:hublog.hubmed.org,2006://2</id>
<subtitle>weblog</subtitle>
<link rel="alternate" type="text/html" href="http://hublog.hubmed.org/" />
<link rel="self" type="application/atom+xml" href="http://hublog.hubmed.org/index.atom"/>
<opensearch:link rel="search" type="application/atom+xml" href="http://hublog.hubmed.org/cgi-bin/mt/mt-search.cgi?IncludeBlogs=2&search={searchTerms}&Template=opensearch"/>
<opensearch:link rel="search" type="text/html" href="http://hublog.hubmed.org/cgi-bin/mt/mt-search.cgi?IncludeBlogs=2&search={searchTerms}"/>
<icon href="http://hublog.hubmed.org/favicon.ico"/>
<author>
<name>Alf Eaton</name>
<email>alf@hubmed.org</email>
</author>