Rivet-nuts and furniture nuts work well for this.
Rivet-nuts are exactly like they sound. It is a rivet that you tighten with a special tool and when done it leaves a threaded tube sitting almost completely flush with the surface. Harbor Freight sells a kit that works good.
Furniture nuts are basically flanges that have 2,3 or 4 holes around the perimeter depending on which model you pick up. It is basically the same as a rivet nut,except instead of the actual fasten riveting itself into place you use rivets in the perimeter holes. These are what I used when I mounted my seat. These too dont sit 100% flush,but i always just use a thin rubber washer under them anyways. Lowe's sells these in various sizes.
I rivet nut grasps a pretty small area. Since you are using 'glass I would probably go with a furniture nut. I have the same job to do and that's what I will use. You can turn the furniture nut ( some call it a T-nut) to where the stud is up inside the seat if you have clearance for that,but I like to mount them with the stud sticking down. That way you can let it protrude thru whatever mounting tab you have and it will help locate the seat. I then use rubber washers on both sides,and a regular metal washer before the fastener goes in to the furniture nut. It helps to prevent the surfaces from scratching the finish on your frame where the tabs are,and possibly eliminate a little vibration.
Hope this helps!
Rivet nut:
http://www.rivetsinstock.com/tool-kits.htmlFurniture nut:
http://www.hystron.com/index.php/english/products/detail/15