You could try adding the alias to the 'Player Faction' aswell. That way anything in the 'Player Enemy Factions' will also be their enemy. You'll need to set up the aggression, as you stated as well. Carlotta is unaggressive, helps allies, confidence average. Set her to aggressive or very aggressive... not 'Frenzied'! Unaggressive should still work if the player is her ally and the enemies aren't. Set her confidence to 'Brave' or 'Foolhardy'. As things stand, Carlotta will try to avoid combat if she is outmatched because she is only 'average' confidence. Any guard in Whiterun is likely to 'outmatch' her, as will many other NPCs. As a result, she'll not attack them, even if she is your ally.
It may be complicated for Carlotta too, because she's in the 'Town Whiterun Faction'. Where have you tested her? I'm unsure how she will react if you are attacking anyone else in that faction... that's basically the whole of Whiterun.
I think you're right to avoid editing vanilla NPCs... that's a big no-no in my book.
You could also try Alias_MyAliasName.SetRelationshipRank(PlayerRef, 3) in a stage papyrus fragment to make sure they are an ally. Setting it to 3 will make them an ally of the PlayerRef*. None of this will work unless the NPC helps 'Friends And Allies'. Carlotta does, though. If the NPC is 'Helps Nobody' in their assistance value they may still refuse to fight. This shouldn't be what's stopping Carlotta, though, but even if you get Carlotta to fight for you, other NPCs may not do so, unless their assistance value is set in the quest too. I don't know the script to alter this AI value.
Factions can be tricky. So can AI data.
* Game.GetPlayer() will also work but it's slow, especially if you are calling it on several NPCs at a time. Set up a property in the quest Actor Property PlayerRef Auto. It will automatically fill and is much quicker for the game.