Chris,
Great question, let’s dive right into it. The extra hours of multi engine time do make the student more desirable by the airlines. It used to be that multi engine time was extremely important in getting hired at the airlines, now it is a bit less so. But for many airlines 100 hours of multi engine time is still the gold standard. Yes, both options end in CFI employment at ATP, but not everybody will chose to work for ATP. For whatever reasons some students chose to go to other schools to teach, such as one that is particularly close to home. Those CFIs will have very little access to build additional multi time, so the time they flew at ATP will be all the more valuable. For a CFI that choses to work for ATP, they will build more multi time while instructing so for them the 40 hour option is a great path.
Either way, you will graduate with the exact same FAA credentials. Which path you chose really depends on what you want to do after your time as a student with ATP.
I hope this helps, please follow up if you still have unanswered questions.
Chris