I always load emulsion in. It tends to match the curve of the film so loading is easier and there's little chance for the film to buckle. Also it means if I do touch the film, it's likely on the base side. However, this is very much personal taste.
Typically, the way most steel reels are designed, the film doesn't touch those bent ends, because they are bent in toward the center as well as down.
However, if one starts the end of the film a little oddly, for example missing the clip and just stuffing the end into the center of the reel, it may be possible for the ends to touch the surface. I don't know if I've ever had those marks, but I've certainly done odd things like missing the clip. A few of my 35mm reels don't even have a clip, just a sort of C shape intended to contain the film end. I load film in a changing bag, so I have to get the film started without messing around for too long, before my hands start to get sweaty and annoying (and of course I would rather not touch the film with sweaty hands).