Bertrand Rusell, who literally wrote the book on why logic and mathematics are formally equivalent (Principles of Mathematics).
This doesn't justify the existence of logic and mathematics, it's a program to reduce one to the other. A cool goal, but not a justification for the existence of the two.
Name one atheist that said he is against logic, knowledge, or reason, on your grounds that it's immaterial. You're just putting up sophistic strawmen.
No need if they hold to a materialist paradigm and want to be logically consistent. Once you make that materialist move, you automatically reject all immaterial things. Unless you wish to argue sylogisms and consistency to be Sophist:
1 Modern Atheism is materialist.
2 Materialism rejects the immaterial.
3 Logic, reason, knowledge and the empirical method itself are immaterial.
Conclusion: Modern atheism rejects logic, reason, knowledge and the empirical method.
If 1, 2 and 3 are true, the conclusion MUST be true.
Address the argument, is it invalid? Is there a premise that isn't met? Be specific which premise you see as not being met, or demonstrate what is invalid about the argument.
For demonstration of what I mean by justifying the existence of knowledge, I've been in discussions where atheists I encounter day-to-day will pivot to saying:
1 Knowledge doesn't exist, it's all constructs
This runs into the problem of them not having a way to know this. I ran into this one three weeks ago in real life.
2 Knowledge is the material nerves in one's brain
This runs into the problem of communicating knowledge being impossible, since the nerves in their brain and the nerves in my brain are different and can't be the same.
3 knowledge is the pattern of nerves in ones brain
This runs into the problem of the pattern itself not being matter, thus the pattern itself being immaterial, thus rendering materialism incoherent and self-refuting.
I look forward to the day when I encounter a solid argument that knowledge is material. I've only personally known two atheists that decided to tackle the existence of the immaterial in an atheist framework, and both ended up adopting Plotinus' system. Hopefully God will bring them to Orthodoxy soon.