Train from Salzburg -> Regensburg. Can I stop by Passau?

The reason you are seeing a high price is probably that you are using the Bahn website for a trip via Wels. Austria. You won't usually get those advance purchase German (SparPreis) discounts unless the trip is entirely within Germany (Salzburg is considered a border station for those tickets. Salzburg to Wels is outside Germany.

If you route your trip via Munich, you can get those SparPreis fares.

If you go across Bavaria via Mühldorf to Passau, you'll be using regional trains. If you then use an ICE to Regensburg, you'll get the SparPreis fare for the entire ticket, but you'll be committed to that train to Regensburg. Or you can use entirely regional trains through Bavaria, and the Bayern-Ticket will be valid; then you can stay as long as you like in Passau.

I like to add the IC/Railjet based connections take a bit more than three hours while the local trains (tick "only local transport") take four hours. If I was in for a bargain, I would take the Bayernticket (yes, it is valid for Salzburg) and local trains instead of SparPreis.

Thank you all for your response!

The Salzburg to Regensburg fare is 19-23 euros which I thought is pretty cheap. However, if I stopover at Passau, then the fare would jump up to 50-70 euros! From what I understand, I can just use the Bayernticket to get from Salzburg->Passau->Regensberg right?

Re: "catching the next one using my ticket?" No, if you get on a RJ train with your Bayern ticket, it's not accepted. That announcement is made in German and English. on the train and in the station.

You can get a ticket from Salzburg to Passau on the same journey with a transfer at Wels for as low as €9 from the Austrians.

https://tickets.oebb.at/en/ticket

I think I'm going to book the train from Salzburg to Passau for 9 euros via the Austrian train website. I assume they share the same train right for that route?

Then, from Passau, I'm going to take a 5 euro flixbus ride to Regensburg. I should have about 4 and a half hours in Passau. Do you guys think that's enough or too much?

Thanks again for your help!

If you want to stay flexible, regional trains depart Passau every hour and a ticket to Regensburg is €20. According to the DB website, you could still book any ICE train from Passau to Regensburg tomorrow for €19, but I don't know if that's always the case.

For a quick glance, four hours are okay. The town was partly built by Italians, so it's different from other old German cities. Blocky buildings that look very modern. But aren't. Walk the Inn promenade and visit the baroque Stephansdom and the five organs in there. There are of course lots and lots of other great sights in Passau, which you can't cover in four hours.