By that definition there are many "most scrambled" positions such as "super flip" that need at least 20 turns to solve (estimated to be around 300 million) - see http://cube20.org. However, this is only a very small subset of scrambled cubes. I suspect this is not what the original question was asking?
All my solvers check that the scanned cube is valid before attempting to solve it. This was originally done to ensure that errors would be detected that were caused by, for example, changes in lighting conditions, shadows and reflections during the scan. However a scanned cube that is invalid as the result of a piece put in the wrong way is detected and treated in the same way. The robots just report the error with a message asking the operator to request a re-scan.
I guess thats down to impatience more than anything, a few people went to great effort to ensure the cube was "visually" totally scrambled, whereby no two cubes where already alligned, notably Thomas Rokicki who immediately presented us with "Super-flip" (Thanks Tom, very much appreciated!)