I'd personally rather that the phenotypes stay without any inherent advantages and disadvantages. Just because God Emperor K'Reel looks like the most fabulous ant we've ever beheld, doesn't mean that they're going to be remotely similar to terrestrial anthropods or to other anthropoids in the galaxy. K'Reel might have nigh-impenetrable skin and inspire the people to work, but another anthropoid might be soft, squishy and lazy despite looking hard and tough (like the Vampire Squid's barbs). All of that should remain in the traits section, and is where I think silicon-based chemistry should go should if it ever gets meaningfully added.Silicone based lifeforms could be interesting. Out of all non carbon based life, silicone based has been theorized about the most. If they were to be included, I do feel like planets specifically suited to them ought to be included as well. It would probably be pretty fun to actually think about how to incorporate them. If they did decide to bring silicone based life to Stellaris, I believe that the time would be right to further make the types of life unique. For example, anthropoids might have a bonus to productivity or a bonus bringing down ethics divergence, and so on for each phenotype. Mammals might have an advantage with habitability or something. Silicone based life would have to be extremely specialized, like they can only inhabit a certain kind of planet but to offset that handicap they are given bonuses to leader lifespan and maybe a bonus to energy production. I also firmly believe that there ought to be creatures that can only inhabit the atmospheres of gas giants and there should be forms of life particularly suited to exclusively living on, what would be a toxic world to any other species. Either way, I really would like to see a greater inherent difference between the phenotypes. To me it only makes sense that a bird, a mushroom and a human will have more inherent strengths and weaknesses which are less interchangeable and more unique to their particular phenotype then they are in the base game. The current system will be a nice start but I think that phenotypes should be more than simply cosmetic.
After all, assuming 'rock people' ever gets added as a phenotype, what if I want to roleplay an evolved version of Pyura chilensis? It's not silicon based, but does look an awful lot like a rock.