Sounds as though you have found the actual problem.
The transformer may be in a box but there will be a piece of wire from that to the point of ignition - a great antenna! The transformer may also be operating at a lot higher than 50Hz - incoming mains is rectified and stored at 250 - 300V DC then switched with a free running oscillator which will create a whole series of frequencies in a "comb", that passes through the transformer to provide the 8kV
The ferrites are worth a try - it is a bit of a black art. You can pass the wire through or through, round the outside and through again. If you can get two of different sizes - they will have different characteristics. Fit them close to the boiler. It might also be worth fitting one one the control/thermostat cable.
Even with a balanced flue there could be an internal fan - my boiler has one.
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