What is the difference between the Mogensen-Scott and the Boehm-Berarducci encoding for ADTs on the Lambda Calculus?
The Boehm–Berarducci encoding is often mistakenly referred to as the "Church" encoding. They both start from the same general idea (encode data types by their iterator/catamorphism), but differ in subtle ways. In particular, the Church encoding only represents data types in the untyped setting, only covers introduction, and is not tight; whereas, the Boehm–Berarducci encoding works in System F, covers both introduction and elimination, and proves that the encoding is tight.

For an extensive discussion of the differences, see this post by Oleg Kiselyov.