When I did my Duster I pointed the engine and transmission centerline at the pinion. The pinion was 2 degrees down which is what Calvert recommends for their suspension. In theory that puts everything in alignment under acceleration. But of course the ride height can move around depending on weight so the driveshaft is constantly adjusting up and down. In my car I was able to do that without having to jump thru any hoops. In some cars you can't do it. The engine is either higher or lower than the pinion so the best you can do is make them parallel to each other.

I don't think it matters all that much. If it was me I'd be more concerned with header clearance, oil pan clearance, hood clearance etc. So put the engine where it fits best and then use the u-joints to connect to the pinion.