The order of operations would be layer contents -> filter -> effects -> blend mode -> fill & opacity, so the filter wouldn't apply to the pattern overlay effect unless you first rasterize or merge the layer. And blend modes throw a whole wrench in the works because you're dealing with at least two layers, so you'd have to merge both in order to apply a filter after the blend, which may not be what you want to do if you only want the filter to apply to the top (overlaid) layer. And, of course, merging layers with a blend mode set can sometimes have unexpected results.

I think a Smart Filter would fall in the same place in the order of operations as a normal filter. That is, applied before layer effects, but I'm not 100% sure on that, and I don't have PS handy to test it.