It has been noticed by many people who think they're gluten intolerant that they digest sourdough bread much better. The likelyhood that this is linked to the changes incurred by the fermentation process is high, since, as you said, that's the only difference.
Sourdough is a mixture of yeasts, lactobacter, and acidophilus in various proportions. The latter two will metabolize the FODMAPS, either while proving the bread or in your gut. One of those choices can cause discomfort and the other a delicious food product.
But the difference is a world apart.
The best example is rye bread, which won't develop a crumb without sour dough.
Concerning the fodmaps, it is the usually longer fermentation that reduces those.
True wheat sourdough is hard to find too. Most bakeries put in yeast and label it sourdough.
Commercial yeast vs. starter [naturally occurring yeast, flour, and water]
> The lactic acid produced by the lactobacilli gives it a more sour taste and improved keeping qualities.
I did realise your main point is that it does include yeast, and I agree with that.
Why is that? The only difference between sourdough bread and non-sourdough bread is yeast vs starter (and some people still use yeast in addition to their starter).