I used a rust encapsulator POR-15 for these kind of areas. You will not be able to get all of it on the patch due to welding. I TIG welded all my panels which leaves a small heat affected zone but there still is one. How do you plan to use the truck? All weather, outdoor storage, etc. My truck is fair weather only so I don’t think rust issues will ever come into play in my lifetime.
https://www.flickr.com/photos/advance-design_parts_co/8129083489/in/album-72157631867396207/