Looks like they added a film to the chip although it's probably not necessary. The bumps are probably just bubbles from the film aging from repeated temperature changes which shouldn't be an issue. Kinda like the stickers on the 4890s, there's bubbles everywhere after prolonged use. The area where the SMDs were touching is just a pad to prevent the chip getting cracked or chipped during installation.

Not familiar with that motherboard but those OST capacitors look like they're in good shape for now!