Let me be honest with you, its a specific question w.r.t. a very specific field;
In my opinion:
1. PFTs are freight stations as per PFT Policies based on PPP (public private partnership); wherein they assit railways by helping in building stations wherein the goods can be warehoused and then transported;
2. PFTs are not operating railways, they are merely facilitating the transportation, but still what difference does it make even if it is a railway operator as there is no exemption or negative list entry for railway operators; it is available to only raiiways;
3. The exemption in point no.20 of notification no.25/2012-ST dated 20.06.2012 is pertaining to transportation of goods by rail. Mere creation of terminal cannot be treated as transportation service.
These are my views, you may also refer to a consultant...