Can a bad transmission cause other problems with the car?

Not very likely. There's lots of different "noises" and they're often open to interpretation. Since it was still under warranty, the dealer MIGHT have been looking extra hard to find something wrong, especially if things were slow at their shop. It's also possible they've experienced that noise before and know it's a clue to a potential future problem.

Almost all transmissions in '70s and '80s model cars lasted the life of the car. Today they're built with lighter parts to save weight and money. Add in computer controls and reliability takes another dive. What really interests me is how so many people take for granted transmission problems are a normal part of owning a car. They were not in the past. I regularly drag around a tandem axle enclosed trailer that's bigger and heavier than the '88 Grand Caravan I pull it with. 234,000 miles on the original transmission which has had only one fluid and filter change in its life. I don't even need to have the electric trailer brakes hooked up. Now, Ma's '95 Grand Caravan on the other hand has a four-speed computer-controlled transmission. She's on her second replacement after 130,000 miles. If I tried to pull my trailer with that van, the transmission would explode with its tongue hanging out before I got to the end of the driveway! It's just not the same vehicle.

That makes my case for transmissions having less reliability the newer they are and when unnecessary computer controls are added. On the opposite side of the coin, Subaru is not noted for having engine or transmission problems. If they do, they are fewer than some other manufacturers have. I doubt I would have been worried about a noise when you test-drove the car, especially if you didn't even notice it, and even if there was a problem in the transmission, there's no reason to think the new one will have the same problem.

I was always amazed that my students were showing me $800.00 repair bills twice per year for their Pontiac Grand Ams, ... And they thought that was normal. It's not, well, except it is for those cars. You are taking your worry way to the other extreme. You're worried about a problem that hasn't occurred yet, isn't likely to occur, on a car that has fewer problems than many other brands. No one can predict what will break or cause problems. Well, let me rephrase that. All mechanics can predict what will cause problems on General Motors and Ford vehicles and a few European imports, but for Subaru, no predictions can be made from past experience.

If noises were a concern, I should have scrapped my Grand Caravan 8 years ago. The engine makes a noise like some part is asking to be let out, but people get out of my way when they're walking through parking lots. I just keep on driving.

As for your comment about "pretty good shape with a new tranny", that has nothing to do with anything. The car could be a wreck. A new transmission isn't going to solve that. It sounds like the car was in fine shape before. Anything can break tomorrow. It doesn't matter how old or new it is, how expensive it is, or what repairs were recently done. That's why manufacturers and resellers are willing to give you a warranty. They know you likely won't need it but it gives buyers peace of mind. We're replacing engines and transmissions all the time on all kinds of cars and trucks. That's no reason to avoid a used car and it's no reason to get rid of the one you have. My van doubles in value every time I fill the gas tank, but it has been so trustworthy, I would stick an engine or transmission in it if I had to. No one else would do that.