after a brief talk in the cool irc channel
set the ports the correct way, or the joysticks don't work, but it probably isn't harmful "generally"
if your msx is setup the way the schematic is in the tech manual, then "no joystick"
if however some are different, as it seems to be from the stuff above with some machines crashing hard, then not setting up r7 in the correct way is a programmer fault, it's meant to be one way only, or else it's wrong, I'd call the joyports being disabled wrong.
maybe someone could put up a list of the machines that completely malfunction and the ones that just have no joyport functionality.
having said all this of course, a machine that stops dead when r7 isn't the way it's meant to be is maybe a borked by design machine
either way, just set up r7 the happy way and it'll work for everyone
I'm just going off the pictures in the sony msxtech.pdf it shows an actual ay chip connected to actual 74 series chips, msx engine machines may have subtle variations that cause this to vary from inconvenience to badness.