Hi, yes you can set the quest tracker window's x/y coordinates as well as its width and max height (the height is variable and will resize up to the maximum depending on how many quests it has to display after which it will scroll).
You can also give the player the option to turn the quest tracker off if they do not want to see it by adding it to the options through any plugin that can add custom options such as [CGMZ] Options.
I think you could show the story progress through the quest tracker, though it would not happen automatically as the tracker shows quests the player has pinned so you would need to tell the player to pin the quest that shows those objectives. I can add a plugin command to pin a quest in a future update so that way the developer can also have control over what quests are pinned.