I think the main difference is the student body and intentions of the program. The MSF is usually made up of 5th year students or those with less than 1 year WE. Most of these students will be going into the work force once the program is done. Because of this there is an emphasis on placement and recruiting. A MAE on the hand is going to be made up of students seeking a PhD. The course load and material will be centered around PhD preparation. There most likely won't be a huge emphasis on placement and recruiting so you are on your own to get a job.
It all comes down to who you are and how you think you can network.If you can get the interviews and sell yourself you will be fine. I think an MS/MA in Econ and an MSF will both have a lot of subject matter overlap, but the MSF tends to be more of the main stream degree.
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