Yeah I am not sure how much that extra size will effect your truck. I would drive it with the screw removed and see if you can notice a loss in boost. You could always put sealant over the hole and drill it back out to 1/16th.

 

I am thinking about the FORD RTV sealant such as used on the front timing chain cover. That stuff is like cement when cured. If you don't think the retail stuff is up to the task, drop some epoxy on there. Would definitely make it "like new". A screw could always rust and fall out too. Stainless steel screw?