Often these APIs even look an awful lot like late generation microkernel shared memory buffer protocols. DRI and uring in linux for example.
A lot of the "microkernels are inherently slow" meme is built on how earlier port-based message passing kernels like mach worked.
What the hell is a microkernel here? What kind of security are you talking about?
User space filesystem and network implementations still need access to the hardware. Multiplexing that access is a kernels job. The more you want to separate and hide that between clients the higher the cost.
As far as i understand your argument you are saying "If an application has a dedicated hard drive there will be little overhead"
But increasingly people realize that the performance of writing to a TCP socket in a unikernel also pretty much sucks and you get a much better result as you move more and more of it into user space. For example you decide, correctly, that TCP is obsolete and you switch to QUIC. Now the existence of the Linux TCP stack is of no value to you. You furthermore discover that Linux firewall, traffic control, and routing also kinda sucks, so you start using raw networking. Then you discover that trying to get your frames processed on the right core at the right moment isn't great in Linux, so you just take over the whole net device with DPDK.
Now, nothing in the whole Linux network stack is of any use to you at all.
The same thing can happen with storage. Maybe you started with files on XFS but then eventually you were using disaggregated storage where a service takes over the whole device with SPDK, and all the storage users are talking to the service instead of the kernel.
Chances are the weird corner case where the TCP implementation blows up was seen in a dozen other Linux applications and fixed, but the same case inside your entirely userspace QUIC implementation gets to explode while the boss is doing the live $100M pitch demo. Awkward.
Code that is competing with Linux for performance is likely to be highly concurrent (a big risk factor for bugs) and doing fancy gymnastics with memory (another risk factor) so we're not talking about a landscape where bugs are rare or one where they're very easy to track down.
I believe this sort of thing is one reason Linux is putting more emphasis on safety. As usual for HN this bug already has people saying both "Rust wouldn't catch this" and "actually Rust would catch this", but even if you're quite sure Rust isn't the answer a safer Linux by whatever means makes this argument better for Linux than it is today.
No, they don't. Filesystems don't need access to the hardware, that part is handled by the block device driver. Network stacks (e.g., TCP/IP) also don't need access to the hardware, that part is handled by the network interface driver.