I've been thinking about this some more, as well as reading about it and experimenting, and I'm wondering if I can now answer my own question(s) to save anyone else having to do so!...
A) In v3/R3 of ReplayGain, there was no "Disable Clip-Prevention" box. It acted as though it was UNTICKED, and therefore any tracks that needed clip prevention were automatically given it.
B) This is why you sometimes got a "Warning: Normalisation gain would have resulted in clipping, gain has been reduced to prevent this....." in the log. So the warning told you that Clip_Prevention had been used, as well as giving you the figures.
Have I got it? Is that right or am I just digging a deeper hole f misunderstanding?
Cheers