Update for those doing similar things:
I found that "po-util" works wonders by abstracting all the above things for me. No need to futz with the weird serial stuff on linux, and nicely full featured. Once I'm plugged in to the USB I can just run:
po serial open
< parse result of particle identify, activate sim>
po serial close
po dfu open
< flash firmware>
po dfu close
< let it connect>
< claim device, add to product>
< run tests>
So much better than pressing the buttons, even if you aren't automating anything else. Highly recommend!