As an update to my earlier question, I can now confirm the availability of the rail cargo option for moving a motorcycle around the country.
I eventually completed my 7 week and almost 7,000kms ride around the country and, as I thought, did not wish to repeat the journey South to Krabi from Bangkok, since there's only one rural route aside from the highway, which wasn't that appealing in the first instance.
I booked myself into a 2nd class sleeper berth, and my Forza 350 bike into the cargo compartment on the same train from Bangkok to Surat Thani, for a total bargain cost of approximately 1,900 baht. The procedure was all well explained by the helpful staff in Bangkok station cargo booking office. I was required to present the bike no later than 1 hour before departure time, and 3 staff, who loaded and secured it in the baggage compartment, were quite happy with a 150-baht tip between them.
The top box had to be removed and, I presume, panier boxes would meet the same requirement.
On arrival at Surat Thani, the bike was being offloaded as I walked down the platform, I climbed on and rode out of the station. No dramas, no damage, I would certainly recommend this option for anyone moving their bike around the country.
I did discover, in Pratchuap Kiri Khan, that bikes in excess of 150cc need to be loaded at the main stations where the train originates, presumably because the intermediate stations are not staffed to handle large / heavy cargo.
What surprised me was the number of bikes being loaded, yet they didn't have a jack up platform to save them the stress of manhandling the heavy bikes from the platform into and out of the train. Obviously not heard of health and safety in Thailand.