The smaller the sprocket, the greater the angle the plates must swing every time a link goes around. The greater the angle, the more the plates wear. Also, a 13 tooth sprocket will only last 93% as long as a 14 tooth sprocket with the same over all ratio because the smaller sprocket only has 93% of the number of teeth. Doesn't sound like much, but it makes a difference. A 13 tooth sprocket will only last 86% as long as a 15 tooth sprocket.
By running a larger countershaft sprocket, a larger rear wheel sprocket can be run, and a longer chain. Each 2 pins added to chain length on a TW increases chain life by about 1.3%.
Since chain wear affects sprocket wear, and vic-versa, dropping sprocket sizes and shortening chain compounds the wear rate of the entire system, so a 13/39 sprocket set with a 120 link chain is likely to last only 75% as long as a 15/45 sprocket set with a 124 link chain. Not that both sprocket sets are the same overall ratio, 3:1.
The only advantage of running the smaller sprockets and shorter chain is lighter weight, which for a championship race bike might matter, but for a TW, you'll never notice the difference.