A possibly better metric may be a direct count of arithmetic instructions per second. Space constraint may also be an important matter to address. For example, the speed of computing the number field sieve depends on memory retrieval speed, which in turn scales in terms of space as well as time. Another example is that the matrix computation in the breaking of the RSA key is done in parallel. Elliptic curve systems, on known algorithms and known hardware, guarantee comparable security with smaller keys.
Smaller keys allow faster encryption and decryption and lower-powered devices.
The paper assumes that cost is zero because all the computation was done on borrowed screensaver time.