Yes, it's supposed to happen. What you need to do is look at each warning and see exactly which files it wants to overwrite. Often it will be the 'Readme' or some other piece of documentation, which is unimportant.
From what you have installed I would guess that it's not only not bad, it's actually good. If an RFB patch wants to overwrite something in RFB, by all means let it - they were made by the same team. Likewise RSRDC. You should be fine.
