Yes the PRT has to be checked. Have you not yet done that?
If not, remove it completely from the three hoses and take a good look inside. If it looks clean and normal through each port, pop it into a pan of water and heat it up. You need two see the valve open fully by the time it reaches 90C to simmering.
I'm also reminded of the DTJ - Double Thermostat Jeopardy.
Your engine has a long history of head work. The skimming has been taken to the limit over several changes of gasket and the overheating persists. The DTJ starts when an inexperienced mechanic changes the HG on a later (PRT) 1.8 engine and fits a standard thermostat into the empty housing (behind the head). He probably thinks that stat was removed to reduce the overheating and he's never even heard of a PRT. The result is very much what you're experiencing, gross overheating during even short drives. Maybe it started at the very first head gasket job.
As part of your investigation, I'd suggest you take a look at the upper stat housing. It must not contain anything other than the 'blank/dummy' stat sealing ring.
See this Rimmer drawing for more:
https://rimmerbros.com/Item--i-GRID001696
The PRT system has Item 15 instead of Item 6.
TC