As far as I know editing a save wouldn't affect achievements. I have not tried playing with mods, removing them and testing achievements.
The game doesn't know why the save data changed, just that it did. Editing it shouldn't cause any problems that are not directly related to the edit.
Loshe's quest shouldn't require the scholar tag. Custom characters can not start with hero/villain tags, but they can be acquired (see
here, for example).
The game was designed first for origin characters. The Kickstarter added additional origins, and eventually custom characters were added, for those who wanted greater customization (and obviously, no specific backgrounds or quests, just the added dialogue options due to the chosen tags).
