I've built several Pelican based systems for my various bikes and also have several factory systems. Honestly, I think its just personal taste based on the lines of the bike. Most seem to have some angle to them.
I angled the Pelican 1430s on my R1 to match the seat line.
The Pelican 1550s on my KLR were mounted low and with just a slight angle to match the seat since it was mostly just a pack mule. (
Stock bags on the KTM(as you pointed out)
Here are some stock BMW bags, angled to match the seat. But I think when these get the metal bags they are flat.