It looks to me like the RJ45 jack is taller than the expansion card slot, and the depth of the bump is more or less the depth of the RJ45 jack + the space needed to wire it in. I'm not sure what else they could have done to produce something that fits in the expansion slot. You can always just use a USB-C ethernet dongle if you think you're going to disconnect it every time it goes into a bag.

Just looking at it, as long as its manufactured to reasonable tolerances, you'd have to do quite a bit to damage the laptop via the protrusion. I'm not sure how big of a deal this is. I'd just throw it in a bag and not worry about it, protrusion and all.