Shorting of wires can short out the transformer causing it to explode and send a power surge to homes. A power surge goes into all wiring and the grounding system and arcing can occur. Electrical arcing gets very hot and melts metal fast. Loosing the neutral at the transformer can also cause problems. Can it happen again? Who knows? Does lightning strike twice in the same place? Can another tree fall or be blown over? Probably.
At least you aren't replacing your main panel and a bunch of wiring and all your appliances and electronics.
If you are looking for an expert opinion that will convince the electric company they are at fault and should pony up for the repairs, then an internet opinion won't work. You need to hire and expert electrical engineer to examine the situation and give you an opinion which would also stand up in Court. Sounds like the storm was an act of God and they may not be liable. Contact your insurance company. The electrical contractor who put in your system my not have grounded properly but you need to have an expert look at it. You can still have arcing from surges even if he grounded according to the NEC. Get into court and the contractor and electric company will blame each other and the storm and it won't be easy to recover.
A lot of homes and commercial establishments are built on slabs but when you have plumbing problems, look out.