for example: you have a pdf with several layers. Can you open that file in PS to where it automatically saves the layers as spot channels? Perhaps you know of an action? Just seeing if there is a way to skip the steps of converting layers to spot channels one step at a time.
Layers and spot colours are separate, different things.
Acrobat "layers" or Optional Content Groups (OCG) aren't supported by Photoshop for read or write.
Photoshop also doesn't recognise spot color data when reading a PDF.
Common tools for working with PDF files are Adobe Acrobat Pro and or plug-ins like Callas pdfToolbox or Enfocus PitStop Pro. Those in Packaging prepress also use expensive tools from Esko or Hybrid Software.