This one adds some missions that are at least extended, similar to your first example in some cases:

https://steamhost.cn/steamcommunity_com/sharedfiles/filedetails/?id=1133287457

For things like Lost Towers I don't know of any mods that add single missions like that. But the game actually treats those kind of multi-stage missions as multiple missions in everything except mission count. You could try Covert Infiltration where you have Activity Chains in which you have to do multiple missions and/or covert operations to accomplish a single goal. For example Dark Events can't be prevented by one single guerilla op, you have to do an Activity Chain with one mission to first delay, then a second one a bit later to prevent.