My battery is going south on my 2005 King Ranch and I have not found a replacement that is maintenance free like the original BXT-65-650.
Sam's Club and Sears have batteries but I don't think I can put the original plastic cover back on over the caps. Ford manual says replace the plastic cover. I'm not sure why it's there, but it looks nice.
I guess at some point before I bought my 2005 it had a battery cover. It was missing by the time I took possession of the truck though. My 1997 had that cover and I ended up removing it, no ill effects on either truck. I would not worry about the battery being maintenance free or not, the cover should still fit, just a little looser.
I recently replaced my stock battery about a month ago with a Kirkland from Costco. $72 if I remember right. 1000CCA. The one listed for our truck in the fitment guide is of a smaller battery but has a few more CCA's than stock spec; it costs $49. I got the bigger one and it fits perfectly.
I read somewhere that the plastic battery cover is to protect electronic components under the hood from the corrosion that will be caused by battery acid vapors - also to protect the battery from high heat in the engine compartment--
I am switching all my vehicles to Optima batteries. They are a little bit more in cost but you do not have the acid vapor corrosion that you do with the liquid filled batteries. Even the maintenance free ones still off gas and corrode the wire connectors.