The application is through the UK government website. All UK visas are assessed by the visa processing centre in India. VFS are the local agents who do the groundwork of checking documents and biometric data collection. VFS also affix the visa sticker into the passport under the authority of the British Government. You see the visa application process is most definitely Gov
You actually apply through the UK government website for visas. When the application is completed and you submit it, you are then directed to the VFS website to make a biometrics and documents appointment at Rama 9
If you stay at a hotel in Bangkok which requests your passport, then yes you would be advised to get a new TM30 on return to Phuket. I do my best to avoid giving my passport for this reason. Mostly I'm travelling with my woman who uses her Thai ID when checking in