If the pedal goes to the floor with the engine, therefore servo,operatingthere is either a leak or, more likely, air in the system. this is not normal - to say it is is stupid - worst case could be a fault with the servo!! . With the engine running the brake servo will be operating, hence amplifying the pressure you put on the pedal - regardless of whether its petrol or diesel. ( a diesel has a separate vacuum pump for the servo because, unlike a petrol engine, there is no vacuum generated in the inlet manifold) You need to fix this - do you really want to have the pedal going to the floor whilst braking - or rather not braking! The new piston on the rear would be my favourite source of air in the system so would concentrate on bleeding that line. Be safe, not sorry.
MikeD