Documentation is incorrect or this is bug in WSS 3.0 SP0 that may be corrected in a later HF or SP. MS please let us know which.

Feature.Collection only returns features that are activated. You need to use SPFarm.Local.FeatureDefinitions to return which are available and programically determine which ones are installed and not active.

                foreach (SPFeatureDefinition SpFeat in SPFarm.Local.FeatureDefinitions)
                {
                    if (SpFeat.Scope == SPFeatureScope.Site)

		.....

Documentation seems incorrect. The Documentation of SPFeatureCollection Class states the following:

Use the Features property of the Microsoft.SharePoint.Administration.SPWebApplication, Microsoft.SharePoint.Administration.SPWebService, SPSite, or SPWeb class to get the collection of Features that are activated in the Web application, Web service, site collection, or site.

This seem to be the way it was designed. I support this by pointing to the fact the SPFeatureCollection has Add and Remove methods but does not have Activate/Enable or Deactivate/Disable methods. Also, the documentation for SPFeatureCollection.Add seems to clarify. Here is an excerpt (I added the bold font to draw attention to the pertinent information):

SPFeatureCollection.Add Method (Guid) (Microsoft.SharePoint)