whereas Uniques/NPCs Destroyed records only player kills.
I think you mean player/player ally kills?
Right sorry, replied too quickly there--it refers to player and ally kills (although Warlord and his faction don't technically count as allies in that sense, since they have their own leader/belong to the Warlord faction rather than your controlled and/or general ally faction).
That's why it won't be listed under the unique kills (the Warlord faction has no other effects for you, otherwise for example when they attack Research etc you'd get a ton of alert and also practically unlimited points).
Also i now have no idea what counts as a "boss kill" for the depth leaderboards.
It uses the Bonus list. If you get the bonus points that's where the + comes from. (This is also why players hunting specifically for +'s don't want Zhirov's help in Command! He "steals" your bonus points since he allows you to skip the kill.)
Yeah this is normal, because the history log records events that happened
But the history log does NOT state Main.C as destroyed, unlike other runs.
My bad! Again replied too quickly. The history log for NPC kills is based on the same rules as the NPC kill list, so it will only record player/ally kills. In that case it was Warlord's faction that did the actual kill. This area of the scoring and records runs into a number of logical dilemmas (or in some cases design dilemmas), so it's not 100% consistent.