Hej nisse – the bottom bracket on the Vagabond frameset is threaded, faced and ready to go, standard English thread 68mm.
Yup, the dent in the fork is for brake disc clearance (as long as you’re using 160mm discs).
If I was any taller than 5’11” I’d be on a large.
I’ve always had bullhorns/flats on my road bikes, this will be my first proper try since a kid with drops, but the frame geo just seems to ask for them. However, get the right stem, maybe go a size up on the frame if you’re close to the edge, and i don’t see why a flat bar wouldn’t work.