I elected to not use the kit-supplied bolts/knob-nuts at all.  Instead I used d-shaped bow-eyes that have a single mounting shank (mine were bronze eyes with stainless shanks threaded into their back side) that go down through the thwart (or mast partner), with a washer, lock washer and big wing nut on the bottom side (against the knees). The screw shank on the bow eye bolt is probably 3/8 or 5/16.  I even made about a 1/4 inch deep countersink inset for the back side of the bow eye to recess into the partner, thus no need to hold that when tightening the wing nut. 

Better than all these words and going from memory I just did a quick internet search. I think I used these, and purchased washer, lockwasher and wing nut to fit at the hardware store:

https://rwrope.com/products/bow-eye?variant=41318183370951 

or here are possibilities you might consider (Maybe shank is too long on the bronze? - you might have to cut more threads if you have that capability.):

https://duckworks.com/buck-algonquin-bronze-bow-eye/

https://duckworks.com/seadog-eye-bolt-with-shoulder/

This does make it just slightly more difficult with installation and removal of the partner, but no big deal, and I almost never remove my partner anyway.  Apart from not having any bolt sticking up/large plastic knob visible (I worked hard to keep almost all visible hardware and rigging and blocks, etc. on my dory as bronze/brass/wood), this assembly provides a nice place to tie random things, fenders, etc. on the port and starboard side of the mast.