In general, is a 7200RPM laptop drive slower than a 7200RPM desktop HDD with similar specs? I know it will vary depending on lots of conditions, but is a standard 500GB 3.5 inch WD SATA HDD faster than its equivalent 500GB 2.5 inch SATA counterpart?

According to specs online, the 3.5" WD is around 126 MB/s, with the 2.5" Scorpio Black around 100 MB/s. Looks like the Scorpio uses less than half the energy, however.

It could be because of the physical size of the 3.5": The reading head can cover a longer distance, i.e. more data, at the outer parts of the platters, at the same time.

You are correct. This is also why a newer laptop drive (higher platter density) can be faster than an older 3.5" HDD.