The filling loop is not at all incorrect. They make them with 2 shut offs and 1 shut off. I prefer to fit one with 2 shut offs but what you have is also common practice.
.without seeing the job then the prv indeed will run next to the condense pipe and terminate on to the flat roof
. You should have a scale reduce on the water inlet and a magnetic filter on the return pipe for boiler protection
. a thermostat or programmer must be installed to meet current legislation
.should only have one operational boiler at once, the old back boiler should not be connected to the heating or the gas.
Here are some prices, parts and labour. The gas run would be between £350 - £500.
To change the filling loop, install a scale reducer and magnetic filter. £300
Install a wireless programmable room thermostat £200
Run the PRV around £200
The flue would need looking at as it sounds like they have used all the wrong stuff and messed it right up. I would say you need to be allowing around £1500 to put all the above correct. That's if the installer has done the system conversion correctly also.
The flue through the roof should have a pitched angle led flashing which slips under the tiles on a pitched roof or a fat roof flashing on a flat roof and felted over. Also a proper vertical flue terminal. A hole can not be simply cut and the flue poked through.