Epoxy blobs tend to be more about cheap mass-production than anti-reverse-engineering. If you're getting a custom chip manufactured, it's often easier to just stick the die straight on the board than it would be to have it put in a package, then put on the board.

How is the bonding from the pads on the die to the pads on the PCB accomplished? Sounds easier to do with packaging compared to PCB for me.

Exactly the same way the die connects to the pins on the package (usually fine wire). Then they cap it all.

Epoxy enhances reliability by keeping the chips hermetically sealed. So when your kid barfs on his favorite Furby it still has a chance of working, or gets thrown by the family dog against the wall.

They are fun to play with from a hardware poking perspective.