Hi,
After speaking to a Senior Manager at KLM and an apology for how my case had been dealt with I can confirm:
If your flight is KLM then Transavia it is true that you cannot pay for hold luggage online and must pay at the airport. So say GLA-AMS-SOF online baggage calculator says £40 per bag paid at the airport. However as you cannot pay online you must be offered the online price which would be I think £25. All KLM baggage/check in agents have been informed of this.
Hand Luggage: It is the allowance on the airline who your first sector is with: So in the example above it is KLM and one bag and one accessory. So you would be allowed this on your Transavia flight even though there's is just one bag. Again all staff have been informed of this.
I hope this information will help other passengers who buy a ticket with KLM which is KLM flight transferring onto a Transavia flight.
Thanks
Scott