not much differences in difficulties, which can be modded.
I should probably list the things that can be modded somewhat easily about the alien missions to throw a few ideas around.
1) You can straight up prevent some of the harder missions from spawning on lower difficulties using minDifficulty in the mission script.
2) The general way to alter mission's parameters for different difficulties is by creating duplicates of mission scripts. Say, for example, you have a hard mission that you want to start appearing in january on veretan+ but in march for the difficulties below. The way you do this is by filling in the mission script, giving it firstMonth = 0, lastMonth = 1 and minDifficulty = 2. Notice this mission would only appear in january and february and only on veteran+. Then you make a copy of this mission script but with firstMonth = 2, lastMonth = -1 (forever), minDifficulty = 0. This one will be exactly the same, but will spawn from march onwards and on all difficulties. So on veteran+ you will have this mission spawn staring january (technically those will be two different mission scripts, but they behave the same from the player's perspective) and on beginner the mission will only start appearing in march, later into the game.
3) You can also use conditionals and duplicates together to lock harder missios behind research, but only on lower difficulties. Say you create a mission script with researchTriggers = STR_THE_ULTIMATE_THREAT: true, label = 1 and minDifficulty = 0. This mission will appear on all difficulties, but only if the player has researched the ultimate threat. Now add a duplicate of this mission script, but without a label, without researchTriggers, with minDifficulty = 2 and conditionals = -1. This one is exactly the same but will spawn regardless of research, and only on veteran and above. Conditionals = -1 ensures that both missions never spawn at the same time.
My explanations can be a bit hard to read since my english is quite bad. The mod's selection of languages implies you speak russian? If this is the case, I can explain these things in russian.