Followed the tutorial, worked fine for myself, I get what you're trying to do now. So the modifier stack is just a way to replicate FWN without using an external script - you want to do it this way for sake of non destructive. You're using highpoly and lowpoly in regards not for normal map baking but rather lowpoly to…
Loop stuff I don't fully get Not sure exactly what you mean by "support edge loops" but I guess its some split loop or loop shift thing- I get stuff easier with pictures. If its very specific but you do it all the time, maybe take the time to either write a script or ask people here in the tech talk section to either do it…
If you want to save yourself the hassle of writing a baking animation script yourself, there's a website scriptspot with dozens of scripts that do just that.