I've only scanned your messages from the start. As I understand you needs sep's from composite pdf's with live transparency (?).
If you have InDesign I think it would be simple. Place live pdf's into ID.
ID is much more fluid in terms of output - support placed multiple pages, define output page sizes, create print presets, print separations...
You have mentioned PS & Illy. You might need to subscribe to CC - well worth the investment if it solves major obstacles imo.