Do you have a link to the Arduino IDE code? I would not mind taking it apart... The IDE is just a simple wrapper so it might not be that hard.
Your second option sounds a lot like dependency injection where you need to inject all your data/settings/object into the constructor/Initializing function. (That will be a lot of work cause I have hundreds of settings.)
thinking of it, I could use a define statement that specifies the board type and configures the config file based on that. Might be the best option as the user starting out with the library will then not see the hundreds of settings and get confused by it.