You may be right regarding the impact on RCS, I don't know nearly enough about how the whole thing works to say one way or the other.Just an uninformed guess here but a CFT will not have the right angle traps where a pylon is hanging from a wing as such you'd think a CFT would make a lower addition to the radar signature than drop tanks. Having said that we are talking about an aircraft that already has a fairly large signature (guesswork here) compared to the 5th gen airframes is this a pretty pointless argument?
If the modifications done under Have Glass and Have Glass II were significant enough to be considered militarily viable, I would think the signature reduction would be a pretty sizable reduction from a baseline F-16. Happy to stand corrected though, as I mentioned earlier it's hard to find decent info on the programs.
Also worth considering would be factors like supporting assets (EW etc), capabilities of the opposition, etc. These things will be pretty relevant as to the viability of an RCS-reduced platform.