I can see and understand the output shaft seal going bad and leaking trans oil out, but I have never heard of the shaft itself popping out. Weird!
It all depends on what the shop did. If they only popped the shaft back in and topped it off with trans fluid, then it should be fine. You can't really damage a trans running it dry. Most people would notice the car not going anywhere and shut it off.
We need to know what the mechanic did. That would help in diagnosis. But the car starting out in 2nd gear almost seems like its really starting out in limp home mode gear which is actually 3rd gear. Can you verify that the trans electrical connector is connected. It should be located below your air filter/box cleaner.
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