> Yet, we all trust these things.

Yes! Because of two words. Consistency and Reliability.

All the physics equations, we trust them not because they are pretty, but because they have been consistent with experiment. Simplified models of transistors are also consistent within a temperature range. Boolean Logic is also consistent, the Turing Machine is consistent,…, the electronics inside a chip is reliable. The instruction set is reliable, etc,…

> Chip manufacturing is so complicated that there's probably no single person who could understand the entire process, from end to end

I strongly doubt that. The actual theoretical knowledge is taught at school and you can take an iron and some electronic elements and build some 8bit computer. Modern chip manufacturing is a matter of scale. It’s cumbersome to design with logic gates, so we invented hardware design languages (just like it’s cumbersome to deal with opcodes) and they are reliable. And instead of PCB, we just use a silicium wafer.