>>787518An MHD engine would be really underpowered for an alien spacecraft tbh, they are great for where we at today but even then I see them being fairly quickly made obsolete in most of the fields they are best at by fission fragment engines. You wouldn't get between star systems in any reasonable timeframe using them.
Realistically flying saucers would probably be helicopters since that's the easiest way to have a big object hover without glassing the ground beneath it. Maybe they just look like saucers because they have wings on their sides which are spinning really fast.