The rational justification for defense of the individual is all persons are individuals and rational persons as individuals would be rational to empower the individual. It's clearly rational to empower the individual but this can also go too far and become dangerous to the majority of individuals.
The balance is you want to not constrain or restrict individual growth and development. This means involuntary ignorance at least in my opinion should be made voluntary or at least a lot less involuntary. By allowing people to make wise decisions more often and by giving AI access to all we can actually improve all individuals. If all individuals improve then everything those individuals touch gets improved and because everyone is connected and increasingly so each day, it's a way to improve your future.
You are right that individualism doesn't belong to science because science doesn't answer philosophical questions. Science answers more fundamental questions about how stuff works. Engineering answers the questions on how to build stuff from the knowledge of how stuff works. And philosophy gives us the reasoning, the logic, the ethics, from which to build stuff which works and is long term sustainable.
So it's not enough to build a new society, but we have to build a better one. We need a new era of Enlightenment to even attempt to build anything better than what we have. Decentralized oppression and ignorance isn't better. Look at the Internet and you see a lot of ignorance, disinformation, and not a lot of improvements to society and life comes from that.
Yet the Internet also has search engines, Wikipedia, word processors, blockchains, and more, which help people to research better, think better, work better, etc. So we need to build the tools in my opinion with pro-science in mind, with the deliberate intention to increase participation not just in capitalism, finance, but also in science. It's not enough to simply make people rich in $$$ by these massive wealth transfers like we see with cryptocurrency, but we also have to make people rich in knowledge which is actually harder but also longer lasting, sustainable, and will have the residual effect of improving ethics.
So the question "how stuff works?" is for you more fundamental to the question "how to live properly?". I don't think that's really true. Thus science actually deals with less fundamental questions.
But how do you decide which one is "better" if science doesn't deal with value systems?
If I don't know how stuff works then I don't even know what life is, or what living is, or how to live at all. So how can I focus on how to live property if I don't know what living is?
If you don't know you need to drink water, eat food, require certain vitamins, etc, then you will not live for very long and all those questions about what is proper are quite irrelevant.
I believe it all starts with knowing yourself, and knowledge of self comes from science. Once you know yourself then you can focus on yourself in relation to others using philosophy.
Whatever you prefer is what is better for you. It's not for science to decide what you prefer. Science simply generates knowledge, how the stars work, how physics work, how the human body works.