My two current gen Ultegra Di2 are both noisier than my current gen 105 on my hybrid FX S6. One was spec'd with a KMC chain (Giant TCR) the other came with an Ultegra chain, which I upgraded to a Dura-Ace chain (now-retired SuperSix), so it's not just a chain issue. I think GCN Tech may have even mentioned a theory as to why the newer Di2 may be a bit louder. Both have been dialed in by LBSs mechanics that I trust. And it happened on 2 different Di2s on 2 bikes that are one year apart, different models, different LBSs, so to me that is more than coincidence.
I can tame the noise by applying Rock n Roll Gold every 30-50 miles. But in the dusty desert that is SoCal, it gets a fairly noisy at the 50 mile mark. The quietest I can get it is when I use the wet style lube (one drop per link). Then it's dead silent. But that stuff really attracts dust and converts it to grime very quickly. And then it's a pain to have to clean and reapply. Which is why I settled on the RNR Gold. Yes I apply it every other ride, but it's a pretty easy backpedal, apply, backpedal, wipe dry. Takes 3 minutes, gets it 90% of the way to the near silence of the wet lube, but with less effort and less grit/grime.
I do that for the SRAM eTap too, which keeps the noise down, to the point where I don't think it's significantly louder than the Di2. At least I don't notice it on my rides (I switch between the TCR and S3 every other day).
A friend is trying out SCC Tech Slick lube which is expensive (for lube) at $25 for 2oz. But apparently according to early reviews it applies like a wet lube (i.e. one drop per pivot joint), so that bottle should last you a good long while, and all it requires is a wipe down after every ride. They claim you don't even need to deep clean the chain prior to first application (though I will), and that if you wipe after every ride, road bikes can get 200-400 miles between reapplications (they really stress the wipe the chain after every ride part). When I run out of my RNR Gold, I may give SCC a try.