I can't speak to the different layouts of the slabs but the parenthesis around the W is explained easy enough. The bottom slab is one of the burnished coins that actually has the mint mark. The top slab is simply a regular no mint mark bullion eagle. It was sent in to be graded still in a sealed monster box that had the west point straps on it so it could be identified where it came from and who ever had it graded paid for the (W). You'll also see the ones out there that have (S). No different than other bullion coins, it just went to the tpg in a monster box from San Fran. Just another variation for the slab collectors. To each their own. Some people like them simply for the fact it makes them easy to handle and look at. Plus it adds some variety over just straight silver stacking--variety, spice and all that. Especially if you pick them up slabbed for the same price as straight bullion. And regardless of what the crotchety old collectors think; there is a market for slabbed bullion of different types. Not everything is Morgan dollars and old copper.
I don't see anything wrong with either of the two pictured slabs....except that they have a meaningless "First Strike" label. I presume that's not what you're talking about though.