Please don't let me stop you from sharing the knowledge.
Well essentially, if you have shuffled the alienmission List, and have a specific Mission as the first Mission of the game, since the behaviour so far was,
that the first Race and the first Mission in the Missionlist will be executed as the first Mission in the game, then your Mod is broken.
Which is the case with my Hardmode Expansion Mod and also with UFO Redux.
But this is not a big bother, since we only need to redefine those Missions, and can let them execute with the normal defined Alien Research Mission.
This opens up a lot of possibilities.
Since you can let the normal alien missions run as normal and define all the Missions for Custom Factions as seperate Missions, which will be executed ontop of the normal ones.
It also opens up the possibility to let research topics trigger Missions, which is awesome.
For example in the FMP you could bind your "Alien Diplomacy" Missions (the one with the golden UFO) towards a specific research Topic, which for example, requires a specific Item, which needs to be researched first and also needs to recovered from another mission which is sceduled ba something else.