How does the ground line get driven high to burn out like that on the 494?
Also, the SMPS transformer isolates the drive transistors from the 494.
the SMPS fets might draw more current from their gates than the 494 could handle before those SMPS fets blew.
The drive (pulldown) transistors are directly attached to the 494, pins 9 and 10. The SMPS mosfets gates are attached to the drive transistors via the gate resistors. The 494's only link between the mosfets and itself are the drive transistors, and if they blow or short they can kill the 494. I think it's most likely your amp has a transformer winding short. It's a VERY common problem with these newer amps because the transformers are so much bigger than what was in the old (weak) amps back in the day. They vibrate alot more due to the higher SPL levels too than the old amps could produce so even your average setup these days has enough vibration going to cause a transformer winding to rub on itself until the enamel coating is gone and cause a short which will sure blow the SMPS mosfets quickly when attached to a large source of current like a car battery.
Not sure why you are investigating this so heavily? Just curiousity or because you are trying to get someone else to pay for the damage?