Some rear main seals are part of the bell housing, and other times they are part of the block. If it is part of the bell housing, it is normal to replace them, if and when the bell housing is removed for service. It is also normal for them to let loose, if the person doing the work isn't familiar with the replacement procedure. You are lucky that the leak didn't ruin the clutch facing also. It takes a lot of force to bend a crankshaft, so I rarely ever consider that a possibility unless there has been some catastrophic failure, such as the BX24 engine being discussed in this Kubota forum. It is unconscionable to charge a customer $1100 after they were quoted $650. The normal is no more than 10% deviation, unless you contact the customer first and get an approval. In many states, they have regulations governing these type of overcharges. What good is an estimate if they don't have to abide by it?
Dusty