Went to get oil change and transmission fluid was drained.

You’re half right, however, that’s not practical on a lot of today’s vehicles. The 4Runner has a dipstick they should check it, but there’s vehicle with drawn out oil check processes, for example full operating temp then 2 minutes of idle time then turn it off and pull the dipstick and allow it drain down for exactly 5 minutes then check the level - that’s your process for an accurate reading. A lot of cars have gone away from dipsticks in general and use sensors with an MMI display. Check the oil is part of doing the job correctly, but it doesn’t fit the quick lube business model.

 

How did the crank case take 12 quarts? Wouldn't it have been overflowing well before then?

 

Well obviously it needs to.

 

Clearly they don’t need to, you just want them too. Its cost/benefit, the time saved rushing through it and throwing in a specific capacity is apparently worth the occasional screw up. They are in it for money, not customer service.