Well this may be a shocker coming from me, but I was disappointed with the new City.
It just doesn't look like something Honda Pakistan would've done, major cost cutting, feature removal has been done on the car.
They removed a couple of things from the Civic as well, like the steering wheel controls, original deck (which they added recently) and cruise control. But gave us other goodies like a good interior fabric (talking about Oriel here) & extra map lights.
However I don't believe Honda Atlas compromises on build quality, at least they did not with the new Civic; and I've had my car for 2+ years now without a single issue Mashallah.
BUT as far as the new City goes-- I don't think an engine sheild should have caused this. An engine sheild really doesn't keep "water out", its more like a splash sheild built for keeping the bottom side of your engine & transmission clean.
Quality control has always been the highest with Atlas, the quality of the City seems fine but the the car certainly looks starved of some extra goodies like the Indian version. Anyhow, I wouldn't buy the car at the price of 1.3-1.4 million, I probably wouldn't buy the Corolla either.
Anyhow, I believe the OP has been sold a lemon, too bad our country doesn't have laws to protect consumers in such cases.