The idea of the Main Bonding is to bond all metallic services to the installation's electrical earth where they enter the house. This is so they can't introduce a potential from outside. If not done, it might be possible to get a shock if you touched e.g. a water tap with one hand and an earthed kettle with the other.
As you have bonded then where they enter, they can't introduce a potential from outside, on a pipe further into the house. So the fact that some of the pipes might go from copper to plastic inside the house is not a problem, as they are not connected to an outside potential, once inside.
There is a similar point about supplementary bonding in the bathroom. Again, you bond the pipes to the CPCs when they enter the bathroom; that done, bathroom becomes an equipotential zone, and any potential brought into the bathroom (e.g. a fault on the CH pump affecting a radiator pipe) will bring all the other parts to the same potential, so you can't get a shock from touching e.g. a radiator with one hand and a tap with the other.
Bonding round the boiler is also similar; if the boiler case, and all the pipes round it, are all bonded together and to the CPC of the supply, a heating engineer will not get a shock from touching e.g. a pipe with one hand and the case with the other, even in the event of a fault which makes one of them live but has not operated fault protection.