Player modes 1-6 can’t be clipped to a layer below. SPA needs to throw that layer away and create a new layer as part of the face detcetion and alignment process. It will copy the layer mask, layer styles, and smart filters over from the prior layer (need to check “use smart objects” when batching for smart filters to work). However, there is no way for SPA to know that the layer was previously clipped to a layer below so it doesn’t know to reclip it. I looked for ways to do that but I don’t think it is possible.
So you will need to use layer mask to add transparency, not clipping masks.In most cases you can get identical results.If not identical, you can typically achieve similar.
In your case, you need to move the player layer back into the SPA player group where it belongs. Then you need to use an additional mask on the SPA group with the transparency of the “clip layer.
In your case, I was able to get the most similar results by also moving a couple other layers into that group too. I sent you an email with a link to the file. Much easier than trying to explain it.
Anyway, you have to work around this limitation and adjust you templates to work with SPA if you want to do this type of complex transparency. You can also use nested group and add additional layer masks to the nested groups.
I realize that certain designers like to clip rather than use layer masks. However, it just is what it is. You need to conform their designs to work with SPA if you want to use those designs with SPA. If I had a way to make it works with clipping masks then I would… but I don’t.