The main difference between those two is that the first proposal: Front-running protection via shielded mempool for OP Stack using threshold encryption (Stage 1: feasibility study) was focused on research and evaluation of implementing shielded/encrypted mempool by threshold encryption.
Mission Request: “Implement a prototype of an OP stack chain with mempool encryption” is focused on the actual implementation of encrypted mempool into the OP Stack and is a more general proposal that is not limited only to threshold encryption, but the mission will allow for the eventual evaluation and implementation of different solutions + evaluation of the results once implemented in the OP Stack chain.