I used parallel port as I/O interface in couple projects, and it works flawless. That is is in same chip with sound generator makes no problems. It is actually independent port, and sound generation will not affect it at all. Actually, on Atari ST there is no other port, where you can hold same state for desired (up to endless) time.
I made EPROM programmer, graphical display driver via ST parallel port. And may do anything where 8 bits are enough. In case you run SW under TOS need to care to prevent activation of printer related TOS functions.
But I don't think that whole idea is much good. Bad side of parallel port is that no separated input and output pins - at least no 8 such. Better would be to make some extra port, with independent inputs and outputs, and number of bits can be even bigger than 8.
Also, using very old computers for some serious control is not good idea because low reliability. So, all this could be mostly in some experimental, educational purposes.
I'm not against GMO, I'm against that children play with fire.