You are correct that with two different PNRs Delta is under no obligation to accommodate you if you misconnect. However, as a matter of practice as long as both flights are Delta they will get you to your final destination, they will even check your bags to CDG when you check in at SJC (just make sure to ask).

I've been in this situation, and the agent didn't even mention the separate PNRs (mine was split because I needed to mix revenue and award legs), they just put me on the next flight.