Zephyr is an "OS" in pretty much every conventional sense. What you're saying, I think, is that a default build of Zephyr on a no-MPU device is a single shared .text segment where all the threads and other OS-managed objects are app-created by C code. So... sure, it's a library and an OS. And even when running on a system with an MPU/MMU, Zephyr tries hard to present that same API (i.e. function calls into the kernel become syscalls automatically, etc...), so the illusion is a fairly strong one.

And given the target market (even the biggest Zephyr targets have addressable RAM in the megabytes, not gigabytes), there's no self-hosting notion. You build on a big system and flash to your target, always. So there's no single filesystem image (though it supports a somewhat limited filesystem layer for the external storage these devices tend to see) containing "programs" to run (even though there's a ELF-like runtime linker to use if you want it).

If you want it to look like Linux: no, that's not what it's for. If you want to target a Cortex-M or ESP32 or whatever on which Linux won't run, it gives you the tools you expect to see.