If you've got a 50 layer image then each time you open a file, I believe the kernel has to look for that file in all 50 layers before it can fail with ENOENT.
It depends on your OCI engine; but this isn’t the case with containers. Each layer is successively “unpacked” upon a “snapshot”, from which containers are created.
A container runtime could optimize for speed by unpacking all those layers one by one into a single lower directory for the container to use; but at the cost of using lots of disk space, since those layers would no longer be shared between different containers.