I had typed a lengthy introduction to an explanation, but realized I don't know exactly where all the bits are going in a high-res low-bitrate image. All I can say with confidence is that if you squeeze a high-resolution image into the same size as a low resolution image, the low resolution image will look better. The high resolution image will basically be reduced to storing DC coefficients, so you'll see these giant 16x16/8x8/4x4/etc. pixel blocks of solid color, with maybe a bit of pattern on them that barely correlates with what the original looked like.

Maybe it comes down to the per-macroblock overhead; maybe fewer blocks total in the lower resolution image allows more bits to be allocated to frequency coefficients instead of DC offsets.