At the client side, a feature layer can't be attached to a group layer, it's always directly attached to the map.
If you publish a map service including group layers, you will see the group layers hierarchy if you are using an ArcGISDynamicMapServiceLayer but you won't see the group layers if you create feature layers.
That's the default behavior. Now you can use the event Legend_Refreshed to customize the legend tree.
From my understanding, in your case you should get twice the same layer legend : one coming from the ArcGISDynamicMapService, one from the feature layer created for maptips. In this case, you could remove the feature layer legend (or to move it in the right location in the ArcGISDynamicMapService layer legend )