The cool thing with using Linux is that you can use the "-s" option, so you don't even need to press the program button.
If I understand this correctly
There are many computers each having a connected teensy and they are headless linux-based?
Yes, we need to update the code on the Teensy via ansible. (https://www.ansible.com/)
Quick supplemental question:
The export sequence export two ex files,
project.ino.with_bootloader.yun.hex
project.ino.yun.hex
Which one do I want?
Neither, since it's not built for Teensy. Try selecting the Teensy board, you'll only get one hex file.