Why are the pads different for THT / SMT components in Eagle?
The features in the PADS layer goes on all layers of the PCB (with actually some additional modifications when you're using more than 2 layers, such as having a smaller copper ring in the inner layers instead of the large pad). SMD components, though, exist only on one side of the PCB. So their pads go on TOP or BOTTOM depending on which side the component is on.

As an aside, be careful when enlarging pads. Go with lengthening the pads and not widening them, since that could reduce the space available between adjacent pads and make soldering it harder, even if it still clears the rules for the fabricator. Also, it become counterproductive to leave more than one or two millimeters beyond how far the IC pin is expected to go. The extra exposed copper makes soldering by hand slightly more tricky.