These are the sort of questions which are the reason that this is not a DIY discussion board. Given my understanding of the forum rules, this thread is only allowed to remain open because you have explicitly stated that you will be hiring an electrician to install the equipment which you decide you want.
With this in mind, I applaud your decision to educate yourself and will do my best to answer your questions, but you really don't fully understand how electricity works.
I don't get this. If the system is grounded, why would a person touching a circuit conductor and anything conductive to earth will likely get shocked?? Were you describing the normal ground fault where hot line touches chasis? Or were you describing path of electricity from the pole utility ground rod passing through the soil and inside the house? But how could there be electricity in the pole ground rod when it is grounded??
Electricity flows in a complete circuit, from the source, through the load(s) and back to the source. If you don't have a complete circuit then you don't get electric current flow.
Consider a bird sitting on a high voltage wire. There may be many amps flowing through the wire, and the wire might be at several thousand volts, but the bird is not part of a circuit and thus no current flows through the bird and it doesn't get a shock.
The same is found with electrical systems. If you have a true _ungrounded_ transformer secondary, then very little current flows through the _first_ connection to ground. There is always some current because of capacitive coupling which will complete the circuit, but in small ungrounded system you could touch one hot wire while standing in bare feet on wet sand and not get a shock.
By connecting the center tap of the transformer to a ground rod, a hazard is created by making the soil a possible circuit conductor. In general the benefits of such grounding outweigh the added risk, but part of this risk mitigation is bringing the neutral to the service entrance panel and requiring bonding of all 'non-current-carrying' metal (eg. water pipes, conduit, etc) to the same grounded neutral point.
If a hot wire touches a bonded chassis, then you get lots of current flow and this trips a circuit breaker.
The system that you describe has the downsides of grounding (creating a circuit path through the soil) with none of the safety details required in the US.
I read so much in the internet about warning not to use Refrigerators on GFCI because during defrosting when inductor runs, it radiates the current away so the GFCI trips. I thought it was normal operation.
Not correct. It is true that refrigerators are known to trip GFCIs, often because of the defrost heaters. However this is not because of any sort of radiation or inductive coupling; this is simply because of leaky insulation permitting a small amount of current to flow from the wires to the chassis. Proper electrical insulation will not leak much current, and a modern refrigerator should not trip a GFCI. The one in my kitchen is on a GFCI with no problems.
If the chassis had proper ground bonding, then this small leakage is not really a problem. But you don't have proper ground bonding, which means that this leakage is going to energize the frame or shock someone.
IMHO if you want the safety of GFCI protection rather than installing proper ground bonding (which I agree is probably crazy expensive and thus not practical) then put the fridge on the GFCI and if it trips, replace the fridge.
Remember I wanted to use an RCBO (Residual Current Circuit Breaker with Overcurrent) device replacing the main breaker in the second disconnect panel in order to protect the main panel itself like what if the bus bar melted the insulation and touches the main panel enclosure. I want the RCBO to trip when this happens instead of fire and sparks.
I can see the benefit of that approach, and agree that it would be better than what you have now. What I was trying to say was that you only have limited resources to make improvements. You should spend your money where you get the best improvement per dollar. Maybe the RCBO is the best approach (I don't know the costs), but maybe that money would be better spent on mechanical improvements to make it less likely that any part of the feeder would actually come in contact with the chassis.
Regarding the trip level of the RCBO: you do not select trip level based on nuisance tripping; you select it to protect whatever the RCBO is supposed to protect. You need to decide how much leakage current you can tolerate; if you need to make a system that will protect a person who touches it, then you need 6mA class A GFCI protection. If you want to protect from fire and sparks then the trip level can be quite a bit higher.
Good luck.
-Jon