Use cases include uploading or playing a file while muxing is still in progress.
No. All of the tools in the MKVToolNix package rely on their input and output files being fully seekable. FIFOs, pipes and standard input/output are not. Therefore they cannot be used.
At the moment there are no proper error messages if you try to use a FIFO as an input or output file. However, the resulting files are most likely cut off or incorrect.