I believe that this is a new trip for Rick Steves this year. I haven't done this trip in the past, but I'm also planning on it for this September. I don't have any reservations yet but I wasn't planning to go back to Tallin; cost wise I couldn't see any reason to. I even tried to setup something where I had a single entry exit point into and out of Europe (Copenhagen or Amsterdam) For example Seatle-Amsterdam-Tallin, then return StPetersburg-Tallin-Amsterdam-Seattle, but that didn't seem any cheaper than Seattle Copenhagen-Tallin, and return STPB-Paris-Seattle.
If you do want to go back to Tallin from STPB I believe Baltic Air and/or Estonian Air have once or twice daily service between STPB, Riga, and Tallin. I think the train service between STPB and Tallin is either non-existent or very long, like 24 hours?
The Russian visa problem seems a bit frustrating, I was hoping to add a couple extra days in Russia to the end of the trip, but with the visa difficulties and since I don't have any firm plans for the extra days in Russia let alone hotel reservations it seems like the visa would be a problem. I wasn't really planning to go on to Moscow but was thinking of a couple extra days around STPB. During my research it seems like there are pretty good train connections between STPB and Moscow and also airline flights.
It seemed like there was something on the STPB Hotel web site about services to help with Visas and also arranging side tours, maybe they could help with your Moscow trip?
My current plan is probably to leave STPB on the last day of the tour and spend the extra days in my exit city (Paris, Munich, Frankfurt, etc). I'm assuming the hotel in STPB will be able to help with the Visa since that is the only place in Russia I'll be staying.