Right, a stroke will always go around the outermost pixel that has any level of opacity at all, so if you apply it to the layer with the rasterized glow, it will go around the edge of the faded region. You can make a separate copy of the outline to apply the stroke to. There is a slider in the layers dialogue… I think it's called "fill," that allows you to fade out the pixels, but the effects remain active. Then just put the layer with the stroke wherever in the stack you need it to go.