Setting up and maintaining a custom Linux build for any hardware is pretty complicated. There's just so much complexity hidden under config options. The landscape of Linux for embedded computers is a huge mess of unmaintained forks and hacky patch files.

That's all worth it to have an application processor that can run your Python/Java app. It's probably worth it to have a consistent operating system across multiple devices.

Would you have many of those benefits if you were using Linux on a micro though? I can't imagine much 3rd party software would work reliably given the tiny amount of RAM. You'd basically just be using it as a task scheduler and wrapper over drivers. You could get most of the benefits by using an RTOS with a memory allocator.