It's because of this in QuestTracker.lua
Code:
local function OnZoneStoryQuestActivityTracked(eventId, questIndex)
self:ForceAssist(questIndex)
ZO_WorldMap_ShowQuestOnMap(questIndex)
end
trackerPanel:RegisterForEvent(EVENT_ZONE_STORY_QUEST_ACTIVITY_TRACKED, OnZoneStoryQuestActivityTracked)
You'd have to override that event on FOCUSED_QUEST_TRACKER.trackerPanel if you wanted to stop that vanilla behavior. Active quests don't use setAutoMapNavigationTarget at all, so that argument doesn't mean anything for that context. SetAutoMapNavigationTarget is relevant for non-breadcrumbed quests only.