The Collaboration Portal uses template SPSPORTAL#0, which has the following definition in 12\TEMPLATE\1033\XML\webtempsps.xml:
<Template Name="SPSPORTAL" ID="47">
<Configuration ID="0"
Title="Collaboration Portal"
Type="0"
Hidden="FALSE"
ImageUrl="/_layouts/1033/images/template_corp_intranet.png"
Description="A starter site hierarchy for an intranet divisional portal. It includes a home page, a News site, a Site Directory, a Document Center, and a Search Center with Tabs. Typically, this site has nearly as many contributors as readers and is used to host team sites."
ProvisionAssembly="Microsoft.SharePoint.Publishing, Version=12.0.0.0, Culture=neutral, PublicKeyToken=71e9bce111e9429c"
ProvisionClass="Microsoft.SharePoint.Publishing.PortalProvisioningProvider"
ProvisionData="SiteTemplates\\WebManifest\\PortalWebManifest.xml"
RootWebOnly="TRUE"
DisplayCategory="Publishing"
VisibilityFeatureDependency="97A2485F-EF4B-401f-9167-FA4FE177C6F6">
</Configuration>
</Template>
What this means is that SPSPORTAL#0 does not point to a Site Template in an onet.xml but rather uses an XML file to define a number of sites that are to be created. Here is PortalWebManifest.xml:
<?xml version="1.0" encoding="utf-8"?>
<!-- _lcid="1033" _version="12.0.4518" _dal="1" -->
<!-- _LocalBinding -->
<portal xmlns="PortalTemplate.xsd">
<web name="Home" siteDefinition="SPS" displayName="$Resources:spscore,PortalManifest_Home_DisplayName;" description="$Resources:spscore,PortalManifest_Home_Description;">
<webs>
<web name="News" siteDefinition="SPSNHOME" displayName="$Resources:spscore,PortalManifest_News_DisplayName;" description="$Resources:spscore,PortalManifest_News_Description;" />
<web name="SiteDirectory" siteDefinition="SPSSITES" displayName="$Resources:spscore,PortalManifest_SiteDirectory_DisplayName;" description="$Resources:spscore,PortalManifest_SiteDirectory_Description;" />
<web name="SearchCenter" siteDefinition="SRCHCEN" displayName="$Resources:spscore,PortalManifest_SearchCenter_DisplayName;" description="$Resources:spscore,PortalManifest_SearchCenter_Description;" />
<web name="Docs" siteDefinition="BDR" displayName="$Resources:spscore,PortalManifest_DocumentCenter_DisplayName;" description="$Resources:spscore,PortalManifest_DocumentCenter_Description;" />
</webs>
</web>
</portal>
You could create a custom Site Definition with a custom PortalWebManifest.xml that includes the name other than SearchCenter that you want to use. Or, since PortalProvisioningProvider does not do much more than create sites based on the XML passed into it, you could use PortalWebManifest.xml as a guide and write code that will create the sites how and where you want.