Right, but 9.3.1 Server doesn't support the "FeatureServer" capability, only "MapServer", therefore the sample .config xml's in the SFV 2.0 use this featureserver feature using AGS 10 technology.
So, although the new Featurelayer does work with 9.3 map services, it needs to be configured differently than in the examples because they use AGS Server 10 FeatureServers.
Edit: Sorry, just realized the SFV 1.3 in the title, nevermind my response.