It looks like vl.c was a poor place to do the mux choice. I just wonder why mux option can't be automatically enabled for stdio in qemu-char.c:qemu_chr_parse_compat() or somewhere nearby.
The mux driver grabs the 'Ctrl-a' hotkey, so I wouldn't enable that unconditionally because the chardev isn't transparent any more with mux enabled.
It also wouldn't really help with command line parsing. cheers, Gerd