I really like the sound of this, and the benefits seem sound. Even so, I have a few concerns. To preface the below, missions are the chief way of getting money, high end materials, and (ideally) serve as a way of guiding us towards game play we are interested in. By eliminating board flipping (not the main goal, but still), we will be completely at the mercy of RNG. Let that sink in.
-If I'm looking for a particular kind of mission and I can't cycle the junk out, then... I wait. If that next board still doesn't have anything... I wait again. Right now, the mission boards normally refresh after ten minutes (I think, anyways). Without the possibility of manually refreshing the boards, this WILL introduce the same maddening non-interactive sit-and-do-nothing wait that some missions suffer from into the process of getting missions themselves. I should not need to explain how this is a very bad thing.
-Since you are moving missions to their own separate server, you will probably be able to afford having more activity on said server. I would aim for no more than two minutes between board refreshes. The largest overarching complaint about Elite: Dangerous is the lengthy and seemingly arbitrary waits between activities. Not lowering refresh times if possible, and as far as possible only feeds this issue further.
-If reducing refresh times is impossible, then perhaps try significantly increasing the number of missions that spawn by a consistent amount (minimum of ten?), and provide a good mix of mission types. I'm not sure why, but some factions will only have three or four missions, and that same faction will later have thirty when I return from another mission. Also, it seems like an inordinate amount will be either "boom data delivery", "massacre X", or in the case of the AEGIS megaships "source and return" (BTW, thargoid mission objectives still take an absurd amount of time to spawn).
-The main idea is to create a mission board that doesn't even need board flipping to be viable. People can whine all they want about flipping being "exploitive" but frankly, it's flat out required for players on a time limit. To compensate, either missions need to cycle FAR faster naturally, and/or have a much higher number of missions for RNG to draw from for increased variety. A slight pay increase is nice, but it doesn't do anything about the core reason that people board flip: to get the missions we want, faster; be that for money, materials, or entertainment. Only the first is addressed.