<--From Fluidmaster instructions. (note: they got the tank and bowl labels mixed up)
There is space for the extra nut. First, there is space between the tank and bowl for the gasket to fit, because of the ridges. Second, most toilets usually have like an indentation, like a funnel, in the bowl... so instead of just having a hole, it has like an indentation/funnel and then the hole down there... that gives plenty of space for the nut. The Fluidmaster image is vague.
So, first put rubber washer on bolt and insert bolt through toilet tank, then put metal washer and nut and tighten lightly. Then place tank on bowl and slide a rubber washer, metal washer, and then wingnut or larger nut.
The nut between tank and bowl is optional; if you don't want to do it then just place the tank on the bowl, put rubber washer on bolt, insert through tank and bowl, slide rubber washer, metal washer, then nut.