Of course the 100kWh modules are made on a new line, they are a totally different design than the old modules. That doesn't mean those new lines aren't in Fremont.
You will notice that the "at its Nevada battery plant" portion you quoted wasn't in quotes because Tesla didn't say it. The author made it up because they thought it was true.
In the 2016 Q3 conference call Elon said "I receive daily updates on the 100-hour kilowatt hour production. After this call, I am going to be on the 100-kilowatt hour production line because the demand is high, and we just need to satisfy that demand." I'm pretty sure he was at Fremont for that call.
I'm pretty sure that the Gigafactory is all 2170 cells (both made on-site and imported), and Fremont is all 18650 cells.