I'm not sure how to upload my example. I'll have to figure it out how if needed. Anyway, I am trying to model an angle clip attached to an I-Beam and C Channel. The clip has a slotted hole created using Hole Wizard and the I-Beam and C Channel has another hole created using Hole Wizard as well. The holes need to overlap each other. My problem here is if I use Smart Fasteners two issues can occur. 1. If I choose the slotted hole on top, the back side with the nut doesn't recognize the channel and shows the nut going through the C Channel or I-Beam. 2. If I choose the hole in the C-Channel or I-Beam, the back end matches fine however the head of the bolt is shown going through the slot inside of the clip. 
Smart Fastener Using C Channel Hole
Smart Fastener using Angle Clip Slotted Hole
As I'm sure you know, the typical Smart Mate function places two mates automatically, one concentric and one coincident. I don't know of any way to have this work to the center of a slot, although someone else might. If you don't get any better answers, I'd go ahead and drop the screw in like your top screenshot, then edit the coincident mate, replacing the surface of the bottom part with the top surface of the part with the slot.