A lot of the time, manufacturers have flat rate time for repairs. I.E. if 'Replace Part ABC' pays .5 hours, then you get paid .5 hours, regardless of whether you get it done in 5 minutes, or it takes two days.
For your transmission problem, the flat rate may well be .5 hours. But, they didn't include removing the loader (add .5 hours), re-installing it when the repair is done (add another .5 hours), removing body parts to access the transmission, removing the transmission, reinstalling said parts, etc...I don't work for Cub and I can't say for sure that's how they work, but I do work on some equipment and have run into that before. It's possible that's how the .5 hour job became a two day, thousand dollar task.
In my opinion, this is where a good dealer will step in and help the customer out. Let us know what you find out!