Je.. Hobie16-man y're making quite a mess of your hull transom.

I personally hate silicone for these type of repairs!

Anyway, why don't you use bolts through the wooden plate with there heads inside the hull. Put the nuts on the outside, so on the gudgeons and saw the bolts level with the head of the nut.
If necessary use a less thicker/flatter nut.

Leading and holding the bolts from the inside is a bit of fiddling but is possible.

And for g..ssake, remove all the silicone (at least for the wooden plate) and use epoxy.

Also Hobie has a one-piece rudder gudgeon for the 16 ( about 30 bugs) which will help you with the wear and tear already outside the transom.