If you think think you have enough threads left in the metal plate, the best thing to do is to use it, and the best way to avoid future problems is to make sure the windlass is well bedded down so it doesn't leak, and use a good thread lubricant on the bolt. Tef-gel, Lanacote, or something similar.
The reason Amel put a plate in the deck only for that bolt, is that for the other three bolts there was plenty of room to add proper backing plates under the deck. With the chainpipe right there, there was no room for a backing plate. A bolt and washer is not sufficient to distribute the load from a windlass to an unreinforced deck. Now, since the plate will still be there to help distribute the load, even if you do switch to a thru-bolt, it's not that big a change.
Oh, yes and then follow Lofrans recommendations for rebedding the windlass on a regular basis.
By the way, I have seen people refer to the plate as "steel", but there is nothing magnetic in my deck there, so I am guessing it is stainless.
SM #160 Harmonie