Yes, the LAN staff does scrutinize the tax calculation line during check-in. Thanks to AA (who based on my experience tend to be somewhat sloppy while issuing RTW tickets), the tax line didn't show that I had paid the taxes from SCL-IPC-SCL. The LAN agent in SCL insisted that I pay the taxes. The agent in IPC hesitated and said something about there being a problem but then issued the boarding passes anyways.