Hey, That black plastic O ring is supposed to go in there too. So don't toss is away. The shifter seat sits ontop of that black O ring. Your shifter seat probably fell to pieces and fell into the tranny or not replaced in a prior rebuild.
Now if Marlin's comes with both pieces, then you're golden!
Yup, my new kit from toyota had a white seat...the old one I pulled (I mean vacuumed) out had pretty much turned to dust.