Not sure if the comparison to Conway's Law works. The key goal of layering is abstraction, so that one can be productive without having to know details about the layers below, but much of optimization is about exploiting details in the layers below for gain. Clearly, these goals are in conflict.

After posing a hypothesis, the post talks about security and process isolation. But the problems raised aren't in line with the hypothesis: the challenge in these cases isn't "insufficient communication" between the levels of the stack, but rather a discrepancy between the abstraction's actual behavior vs. a human's desires and expectations about big-picture topics.

These abstractions often compromised by information leakage through side effects that executing code can observe or deduce, leading to the class of vulnerabilities that have long been around, but have received far more attention since Spectre.

Protecting against timing attacks and other side-channel attacks requires the observable state of the system to not vary due to execution in a different security domain. Timing attacks are particularly frustrating, because processes can estimate their execution time even without external timers, so it can compare the time taken between different calls. Cryptographic operations often take special care to avoid leaking information through timing, but the same discipline isn't commonplace in system calls or userland code. And shared caches will leak info in timing but greatly improve performance.

Hardware isolation is an effective solution for curbing timing attacks for systems that don't communicate over a network. It's not sufficient in the case of networked systems, because the network and its connections form another source of observable state that's likely full of unrelated side-effects.