You will see the flow rise is quite rapid and return catches up lot slowly resulting in burner shutting down. With low loss header that does not happen. This problem I believe does not take place with a combi boiler but seen it with a system boiler
You're mostly right.
The return is not expected to "catch up" with the flow temperature. Don't think about the water leaving the boiler, going all the way round the system and coming back before the return "catches up" I had the same thinking for years and never understood it 100%.
The way to think about it is look at the return temperature first. If the return is at 25 degrees, the water then moves from the return through the heat exchanger and then should be no more that 45 degrees at the flow, regardless of how long the boiler is on for the flow should be about 20 degrees or less, over the return temperature. If its exceeding this, ie 25 degrees on return 55 degrees on the flow, then this can only physically happen if the water is moving too slow around the heat exchanger. And that is what the boiler is monitoring to prevent it damaging itself.
The reason you don't see it on combis and most system boilers, is that they come factory fitted with the correct size pump, and an appropriately sized and adjusted auto bypass valve to suit the boiler.
With heat only appliances you rely on the installer specifying, fitting and setting the correct component externally, which often does not happen.
The likes of the 438, in 99.99% of cases is far far too big for the property its fitted in, and your limited on corrective action, considering the average UK house needs around 7-8kw on the coldest day of winter. The 438s are almost never piped right either (ie 28mm primary pipework)
The 418 in the original post, working fine on hot water and not heating, would sound like theres a restriction on the heating circuit, or possibly the pump is getting weak and unable to move the water volume required for heating the radiators, which will be a more restrictive path than the cylinder typically.
As far as the modified PCB goes. Being a heat only boiler, it doesn't have any way of detecting that there is water in the system and therefor no way of preventing dry fire without the use of its temperature sensors.
It fires at around 60-70% of its full rate as virtually all zero governor boilers on radial heat exchangers do to get a successful air/gas ignition mixture, it then ramps up to a high rate, so it can monitor the temperature rise on the flow and the temperature difference between the flow and return, this is how it checks for water content, and to check the flow rate is ok, if its not it will either shut off, or lock itself onto minimum rate to prevent damage. The PCB upgrade essentially just reduced the time spent at 100% output to reduce this happening.
However in every single instance, its either a restriction in flow, or a massively over sized boiler (which will also have a restriction in flow)
Solutions as said, a low loss header can go some way to curing the issue, as the flow rate through the boiler is then kept constant at all times, however that often doesn't address the issue if the boiler is far too big for the property as the water will still heat very quickly overall leading to short cycles.
Sometimes its much simpler, often theres no auto-bypass fitted, or its fitted but not set up right (which would keep the flow higher through the boiler in a similar manner to a low loss header thus keeping the temperature difference between the flow and return stable)
If its only just become an issue recently, then blockages, pump faults are more likley.