I can only answer based on my and my friends experience
Lets get one thing straight - railways is full of corrupt people top to porter level
Having said that railways expect you to collect your vehicle on same day or within 48 hours if I remember correctly and if you fail to do so there would be a nominal storage charge that you need to pay. However its reasonable and does not go into thousands unless maybe you didn't collect for a long duration. I once collected my Unicorn after 3-4 days and maybe ended up paying 200-300 rupees as storage charge ( verify the rate with railways by going directly to parcel counter )
The delivery chalan is the receipt that they give you when you book the vehicle as far as I recollect there is no other challan, when you reach the destination you show the challan at Parcel out- get it stamped - give some small chai pani ( bribe) to potter who fetches your bike - depending upon location you may have to give some chai pani to the security guy at the exit gate as well.
I have not read the pdf document you have attached but I can say that you can safely transport by railways.
Ps: its also in your interest to get your vehicle out of the railway station at the earliest for the safely of your bike