You can built U-Boot with the same cross-toolchain used to build the kernel - and most probably the rest of the user-space of the system.
A bootloader is - by definition - self-contained and doesn't care about your choice of C-runtime library because it doesn't use it. Therefore the issue of sys-calls doesn't come into it.
A toolchain is always going to need to be hosted by a fully functioning development system - invariably not your target system. Whatever references you see to a 'bare-metal toolchain' are not referring to the compiler's use of sys-calls (it relies heavily on the operating system for I/O). What is important when building bootloaders and kernels is that compiler and linker are configured to produce statically linked code that can run at specific memory address.