what kind of php app are you running that requires to be linked against a specific linux kernel
This does mean that you end up with multiple copies of the same utilities and libraries on the system - although docker does have a mechanism to avoid duplication between different docker containers. It also means that if you take your docker container and move it over to a different system with a newer operating system (or a different distribution) all the parts of the operating system it cares about come with it.
The Linux kernel - the part that gets shared between containers - is mostly just responsible for process and memory management, networking and interacting with the computer hardware.