I finally spared some time for the inspection by removing the liner. Fortunately, it appears that the rust is just from the quarter panel rather than from the sill (yet). Here is the picture with the liner removed.
I have inspected the under side of the vehicle too. No rust there yet too. But unfortunately, rust is found on the other side of the vehicle (the rail like structure under the body). But I think it would be OK to let it rust for a few more years.
Anyway, I am relieved that it is just a small spot on the quarter panel so far and it is DIY repairable for novice DIYer.