If I were to speedrun a mission, would I start the timer at the first story mission of campaign, or when the campaign starts?

(Also, does Pirates! and things count towards all missions?)

If you're running a single mission (campaign or otherwise) then you could start an RTA timer when you click the start mission button or maybe use the in-game mission timer. I currently don't have any IL leaderboards, but I could add them if needed. Campaign ILs might be harder to set up, but the training ILs might be a good fit. If you're running a specific campaign, it would make more sense to start the timer when you start the campaign after selecting the difficulty and era.

Which missions count would depend on how an All Missions category is defined. The categories for each campaign currently only require that you successfully complete each campaign specific mission. The extra missions you encounter, such as Pirates! or Escort Duty, can be skipped (exit mission through menus) or failed (warp out of the area without completing the mission). I believe a few campaign missions can be skipped without you being kicked out of your "Clan" (for Lyran), but I decided against it when making the category.

I'm open to having more categories or variables if you find a different way you'd like to run the game.