In our pebble finish we had a major and obvious streak several feet long that only became obvious after filling (I believe from improper rinsing after acid) and we insisted the PB fix it. Now that is taken care of the finish still has areas that vary slightly in color. Mottling is probably the best description. Maybe it's a coincidence but the effect is most obvious in the "regular" shallow end. Much less noticeable on the very shallow areas (Baja shelf and bench) and the deep end. I can pick out the worst spots pretty quickly and they are somewhat obvious to me on a calm day. HOWEVER... I am the one out there paying attention, testing the water, brushing, etc. My wife has not noticed it. It is highly unlikely anyone else will spend enough time looking to notice. Once anyone is in the pool and the surface is moving even I am hard pressed to see the difference. Moreover, I seriously doubt anyone who comes over to swim in the pool is going to care. I suspect you are somewhat in the same situation - although it is hard to tell from photos. All this is to say, take a look at the practical implications and pick your battles. If it really bothers you then certainly don't be shy to push your pool builder for a fix, but I agree with the sentiment expressed by others to consider the risks of your builder repeating the same mistakes or causing other problems.
For what it's worth, I also recently got done with a pool builder who was really difficult to work with and I feel your pain. We had our tile crew back out to the project multiple times and eventually realized that "good enough" was as good as they could manage.
Before this we had a fiberglass pool and the finish was perfect, immaculate, consistent white, but it showed every speck of dirt and minuscule stain! By comparison I prefer the "natural" variation of the new pool.