If we want to create native Linux apps, we need to use glibc C APIs
Well, that statement is false. To write a portable C programming language program, you would use C standard library. glibc is one of the implementations of the C standard library, but there are other implementations. To write "native Linux apps", you can write it in assembly, or use other library, or use a different programming language.
If I'm correct the glibc APIs themselves call the Linux C APIs
System calls are the way to communicate with the kernel. Also with Linux kernel. I do not think I want to call system calls as "C API", it's more assembly API or machine code API, and there is C API built around it.
Is that Linux C API available for programmers or is the glibc the lowest we can go?
Let's say the "lowest" you can go in C on Linux is to call syscall()
.
What do other higher-level frameworks use?
It is specific to that specific "framework". Usually 99.9% of the time any program written in C uses the C standard library available on that system. The build process of that specific application chooses what C standard library to use, and docker shows that applications using multiple C standard libraries can coexist on one system.
.NET, Java, Python,
Python is written in C, for Java see In which language are the Java compiler and JVM written? , I know nothing about .NET .
Do they use glibc APIs or do they directly talk to the Kernel?
If they were compiled against glibc, then they use glibc to communicate with the kernel. But on Alpine, programs use musl.