Throttle body causing transmission problem?

I have a 2005 VW Beetle with a six speed automatic with 85K miles. It has been having trouble shifting into 4th gear. This is most noticeable when the engine is hot and at soft acceleration (city driving) at about 35 mph. It feels and sounds like it is stuck in neutral momentarily and then falls into gear with a lurch and a clunk. I assumed that the transmission is going bad and took it to the dealer. The mechanic says that a computer code is being generated indicating that the throttle body is bad, but none that says anything about the transmission. He wants to replace the throttle body at $800.

I asked for a price on the transmission in case this throttle body replacement doesn't fix the problem because I am skeptical. That price is $5,252! My question is does it make any sense that a bad throttle body, which for a modern fuel injection engine may well have computerized parts and connections, etc, would have any impact on transmission function? I don't really want to spend $800 and not fix the problem, since replacing the tranny at $5252 would to me make no sense at all in a car worth only $10 with a working transmission. In other words, if the throttle body issue is not likely to fix the problem (they say it probably will fix it), I would rather take my chances on a trade in and get rid of the car. What do you think?