Well, there is no way to get around the system. My flight is tomorrow (SFO to EWR to DEL) so I went to SFO to check in this afternoon. The Kiosk recognized my passport but needed the agent to swipe her card, I showed my visa, then I was checked in and printed out my boarding passes. I was good to go.

Interesting thing was that since I requested the seat changes, I tried to use the same Kiosk again to print out the new boarding passes. It asked the agent to swipe the card again! You would think that once you already checked in, you checked in, as your documents were validated! After done with the second time, I went to another Kiosk, scanned my passport and went through the process without being asked again. Maybe even if you change seats, you may have to show your travel documents to get new boarding passes...

Hope this helps

PS. By the way, I got my upgrades. I guess the trip was worth it!