Those settings don't factor in skulls. So any skulls will then have an additive effect. So a HLAI would start off with 1,864 supplies, and with the Bountiful Resources skull on they would also get the same perpetual 25% economy boost as every other player.

Even though most of the 'score decreasing' skulls have 'PlayerUnits' effect targets, they seem to apply to -all- player types for whatever reason. I'm not sure if this was an oversight or intentional. While they have a separate 'skulls' system they also have 'tech' definitions for those skulls as well. It could be that someone forgot to switch off the applying of techs to all players to just using the actual skull system.

The Rebel Leader skull isn't done with a tech, so that would explain why it still only works on the AI. And the Rebel Supporter/Sympathizer skulls tech definitions explicitly target the Creep (AI). However, the Bountiful Resources tech applies to supply depots without any sort of filter. Interesting note: the tech doesn't have any effects for supply hooks (like the ones on Blood Gulch)