Technically a 2WD RWD car "should" be faster, in that (as you correctly say) energy isnt being lost to drive train drag etc. However, RC car percentages probably aren't as big as we might believe them to be.
Whereas in a real 1:1 car you would definitely notice the difference in power gained by converting from 4WD to 2WD, RC cars in comparison are a lot lot smaller and therefore any gains are a lot lot smaller - if noticeable at all.
For the most part RC cars are massively overpowered anyways, again making any gains very much insignificant. Another thing to bear in mind is that your guy might be losing top speed in his overall run due to breaking traction during his acceleration phase - again something quite hard to notice to the naked eye (or ear), but might account for any reduction in top speed.
4WD offers more grip, therefore theoretically more grip under acceleration. 2WD offers more power into half the overall tyre contact patch.
Lots of variables to consider.