If a module (3rd party or otherwise) is storing its settings in the ModuleSettings or TabModuleSettings using the DNN API, then the settings should be picked up using the Portal Template, if you choose the export content setting when creating the template.  However, many 3rd party developers choose to store the module settings in a proprietary table in the database.  When this is the case, you will need to approach each module vendor and demand that they add the module settings to their IPortable implementation.  Good luck.  :)

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Will Strohl

Upendo Ventures DNN experts since 2003 Official provider of the Hotcakes Commerce Cloud and SLA support

There is a clear line to follow and know that we are speaking about when talking about what is exported.  When you simply choose "Export Content" from any module, content is all that you get.  However, having just tested again using the most recent version of DNN, I was able to confirm that if you export a page or site template, you will indeed get all of the module settings - INCLUDING those that are saved into the API module settings.  Here's an excerpt from the HTML module:

<modulesettings>
    <modulesetting>
        <settingname>HtmlText_ReplaceTokens</settingname>
        <settingvalue>False</settingvalue>
    </modulesetting>
    <modulesetting>
        <settingname>WorkflowID</settingname>
        <settingvalue>1</settingvalue>
    </modulesetting>
    <modulesetting>
        <settingname>Allow_PageWorkflowOverride</settingname>
        <settingvalue>True</settingvalue>
    </modulesetting>
    <modulesetting>
        <settingname>Allow_ModuleWorkflowOverride</settingname>
        <settingvalue>True</settingvalue>
    </modulesetting>
</modulesettings>
<tabmodulesettings>
    <tabmodulesetting>
        <settingname>hideadminborder</settingname>
        <settingvalue>False</settingvalue>
    </tabmodulesetting>
</tabmodulesettings>

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Will Strohl

Upendo Ventures DNN experts since 2003 Official provider of the Hotcakes Commerce Cloud and SLA support