If I understand this answer correctly, C compilers are free to choose
the ABI/calling convention of a function as long as they preserve the
semantics. For instance they can choose to pass a pointer for the
returned value as an argument to obtain copy-elision.
I don't see how you conclude that from the answer you referenced. Calling conventions are a characteristic of the function, as it appears in compiled form. The compiler can do all manner of tricks at the point of call, but changing or ignoring the calling conventions of the function implementation is not one of them. Where it is possible, copy elision for returned structure values (the subject of that answer) does not rely on any such thing.
Does this mean that no one can ever truly know what's the right way to
call a function from a library, even if its C signature is known?
Yes and no. The function signature alone does not convey anything about calling convention (with some caveats; see below), but libraries simply could not work if there were no way to know calling conventions. In practice, it is usually the case that calling convention (and ABI overall) is standardized on a per-platform basis.
Thus, for example, Linux implementations for x86_64 substantially all follow the same conventions. All the toolchains targeting that platform both use that convention for function calls and provide for functions to be called according to it. Compilers for Win64 likewise follow the appropriate (different) conventions.
Windows is in fact an interesting case, however, because historically, it has supported multiple calling conventions. In its case, there is a default convention, and different conventions can be specified in function declarations via extension keywords. The compiler knows which convention to use based on the function declaration.
Additionally, where it is not concerned about interoperability, compilers can do anything within their power. So, for example, when compiling a function with internal linkage, it could, in principle, use whatever calling convention it wants, as it is in full control of both the function and all callers (ignoring the possible effect of function pointers). This is not different in kind from compilers' ability to inline functions. As a practical matter, however, I would not expect compilers to use variant calling conventions under such circumstances, and I am not aware of any that do.
Is this a real concern in practice? Or is it safe to assume that all
the functions with non-mangled names from system libraries always use
the system's default calling convention?
Name mangling has nothing to do with it. That's part of a higher-level mapping of C++ (usually) semantics onto system-level, source-language-independent object-file formats.
Generally speaking, it is safe to assume that where the appropriate function declarations are in scope (from the library's header files, typically), the compiler will generate correct calls. This is an essential interoperability characteristic that is rarely violated in practice. It cannot be construed as a universal guarantee, but in practice, it is not something that you should worry about.
What other assumptions or considerations can I make about the
ABI/calling convention of functions with non-mangled names in system
libraries?
I'm unsure what kinds of assumptions you have in mind, and I suspect you're overcomplicating things. You make sure to include the header(s) from the relevant library that declare the functions you want to call. Having done so, you rely on your compiler to generate correct calls.