I'll put my hand up as I'm both much less fit than normal and much heavier than normal (~3 stones over previous racing weight - for an average height female, that seems quite a lot) - normal being when I used to race in the Alps for a Swiss club and ride back-to-back 300km days in training.
I do find my saddle somewhat less comfortable than previously - when it was not noticed, really - as I feel that I do sit more heavily on the back of the saddle. I use a fairly solid women's saddle (Selle Italia Trans-am and it's more recent incarnations). I would also say that the discomfort starts around 80 -100km, depending on the terrain, and I notice that I start to shift around on the saddle more. It never gets to the point of painful riding just - how to put this? - my sit bones seem to want a rest.
It's definitely getting better as I do more longer rides on the upright (I've been recumbent riding mainly for the last few years and, of course, saddle discomfort is not an issue there) so I would have to say that I agree with your suggestion that lack of fitness/time in the saddle is playing a part since the saddle has the same properties as those I've used over most of the last 20 years or so over much longer distances.