Well, it is fair if all you want to do is mash some data together. Why shouldn't startup times be taken into consideration?
Because with R you can and usually do multiple things with multiple data sources within one session, which effectively dissolves the start-up and load time. Even if reading one file and calculating mean or something with a single script is the only thing you do, you can use Rscript which runs R without loading heavy stuff like the methods package.