I have lived in Phuket 20 years now and I have probably had around 10 of these residence certificates for car or motorcycle purchases or driving licenses. They have always been free , only once some immagration officer asked me for 300 , as soon as I said I would need a receipt he said ok free .
They are absolutely without doubt meant to be free , I have even seen the Phuket immigration office post an article announcing there free.