Yes, everything affects flavor, color, etc. Caprification affects taste and color. Clearly we are talking about figs that are not Smyrna types, since they can't be tasted without being caprified.
In my experience most figs have greater flavor when caprified, but some do not taste as good. Interestingly, for me, Black Madeira has never tasted as good when caprified as it does when it is not. No way to know how much weather, soil, fertilizer, water, etc. affected the caprified figs I have eaten.
That is part of the issue with figs - they are so responsive to their environments that it is very hard to make comparisons between figs grown in different conditions. When figs on the same tree can be honey colored and strawberry colored depending on what week they ripen, it gets a little dicey trying to make dogmatic statements about how much this factor or that factor affects flavor.