Actually in ID4 there was an explanation. Basically all of humanity's computer tech came from reverse engineering alien tech. So our computers worked with theirs because they were based on theirs. Maybe this isn't this best logic, but they did at least have an in universe explanation.
The ultimate security by obscurity. Do you have a 30m antenna? Can you point it exactly at the space ship with almost no error? Do you know what it's code and protocols are? OK, please reprogram Voyager