Computers haven't presented an accurate model of how computers actually work for decades. Compare the surface ISA of anything mainstream since the mid 90s versus all of the superscalar and out-of-order execution happening under the hood.
Deliberate efforts to surface this deeper layer back to the programmer-facing ISA (VLIW, notably Itanium) failed spectacularly outside of niche applications. C and its contenders can't simply hop over the CPU abstraction presented to them without having to map backward from some lower-level model to the surface ISA it's forced to target then having the rug pulled every few years due to microarchitectural changes. It has managed to evolve surprisingly gracefully over decades from tiny 16 and 18-bit machines, sometimes segmented, to 32 and 64 bit machines, and even accommodating SIMD reasonably gracefully via intrinsics (which is about the best we can do at present, as CPUs continue to diverge wildly in this area, though I'm begrudgingly impressed by what modern compilers can do via autovectorization to optimize simple loops).
Do you really need a central directory? The tar and cpio file formats basically append files serially with a small header preceeding each one, and for most use cases this is sufficient.
Seems to be a tradition rooted in the original Maniac Mansion. In Thimbleweed Park the multiple characters became tedious due to having to walk multiple people all over and pass items between them, though I enjoyed being able to see the world through the different lenses of how Ray and Reyes vs. Ransome vs. Delores react to things.
Day of the Tentacle (which coincidentally I've replayed in the past week) executed the multiple characters mechanic the best I've seen, since each character was confined to their own area (past/present/future) and you could instantly pass items between them.
(sorry)