Yes, it means you have to go through the atmosphere, but it doesn't take far to clear. That will effect the calculations some, but not much. What will really effect the calculations though, is the cost of electricity. Generation costs will surely drop below $0.04.
Further, transmission loss can be almost entirely mitigated by generating and supplying the required power on-track.
Launches in favorable conditions (moon and/or planet alignments) would probably make some launches even cheaper. Of course, if the launcher were operating continuously, the savings would be used up during unfavorable conditions.