Vienna~Salzburg~Berchtesgaden Train and Rental Car Advice Please

not sure if it helps, we spent a number of days in Berchtesgaden, last year, and drove into Salzburg twice. the traffic both times was not overly heavy or difficult. there are major roads that skirt the city.
remember to check you have an austrian vignette on the car ( for the toll roads) although I guess the rental car should have this? if not they are available from service stations and I believe they are only need if you intend to drive on toll roads.
I can only assume your reservation at eagle nest allows for getting the bus from the car park?( as the buses that go up the mountain, i think, leave at specific times and leave together) we did not book a tour but managed to get on a bus, without waiting long. ( it was quite busy - in may last year) car parking was at a bit of a premium for us, eg we had to walk a few hundred metres to get near the usual car park. but OK.
while you are touring eagles nest , have you considered looking through the document centre? its also right there at the same car park ( near where the buses leave from) we found it very interesting. the town of berchtesgaden is quaint and small enough to easiyl navigate if you are looking on getting a meal etc before hand. Konigssee lake is only 'down the road' from there and is very nice to visit.
also , if you have a car you might consider the rossfeld panorama road, its near eagle nest and is well worth the few euro ( road toll) for a look out over the surrounding area. the views are similar to what you see at eagles nest but being in your own car you can stop and walk around.

its a lovely area to visit.

hope this helps.

We did something very similar last summer.
Salzburg is quite small and traffic isn't bad compared to where I live in Los Angeles. Any traffic you hit will be just for a small distance and mostly through the suburbs/traffic lights that ring the town. For picking up the car I would allow at least 30 minutes, then getting out of the city will take another 30 minutes (at most), and then the drive to Berchdesgaden is only about 30 minutes.
You'll need park your car and then catch a bus to go up to the top of the mountain where you will catch the elevator that takes you up to the Eagle's Nest. Allow at least 45 minutes to an hour for that process. The lot can sometimes be full and you may have to park on the road.

According to viamichelin.com it's a minimum 40 minute drive from the train station to the site, though there probably won't be much traffic at midday. You'll need the Austrian vignette for this route (takes the toll road around Salzburg) - or an hour going through town.

How much time you need to rent the car - well, that's a crap shoot. But if you plan time for lunch, then you have a cushion. If the process takes a long time, grab sandwiches at the station - or have lunch at the Eagle's Nest restaurant.

I'd recommend using the Westbahn from Vienna to Salzburg.
You can buy tickets on the train, but it is cheaper to book ahead or even buy the tickets at a tabac.
They do have several offers for advance bookings, esp for weekday travel.
https://westbahn.at/en/offers/westbahn-offers/

The national railway is here:
http://www.oebb.at/de/

For them, unlikely you need to do anything ahead. You can buy your ticket at the machines in the train stations or use the customer service office and have an agent help you. Assuming you will pass though a train station on your arrival to Vienna, you could by one then and be ready to go.

Have fun!

TravelBug is not going to the Kehlstein Busabfahrt, where the buses head up to Kehlsteinhaus for the tour. There are no tours from the parking lot a Kehlsteinhaus. She (?) is going to start the tour by David and Christine Harper at 1:15 pm from their headquarters in the Berchtesgaden visitor's center across the street from the Hbf.

Instead of spending time renting a car, which is just going to cost you more anyway, take the RVO bus (#840, Watzmann Express) from Karl-Wurmb-Strasse (to the right as you come out of the Salzburg Hbf, between the Forum buildings) to Berchtesgaden. There is a bus at 11:15, getting to Berchtesgaden at 12:04, giving you just over an hour to eat lunch at one of the restaurants around the Hbf before your tour. If you purchase a BGL-Tagesticket Bus & Bahn from the bus driver for 12€/person, it will cover the bus to Berchtesgaden and the bus back or, if you stay in Berchtesgaden past the last bus back to Salzburg at 7:04 PM, the train via Freilassing.

That makes perfect sense. We all assumed that TravelBug meant a tour that began at/near the parking lot.

The first time I was at Kehlsteinhaus (2000) there were "freelance" guides at the tunnel entrance. I didn't see them there the last two times, so when TB wrote about a guide tour, I didn't think it was from the parking lot. I was already aware of David and Christine's tour. For some reason I exchanged emails with David a few years ago. I think he has the only tour from Berchtesgaden; I think there is at least one from Salzburg. The time mentioned by TB, 1:15 PM, coincides with the time of Davis's tour, so that must be it.

Thanks to all for your responses. Yes, we are taking David and Christine's tour. We want to have the rental car, because we plan to explore that area for a several days before touring Salzburg. Appreciate everyone's input!