It kinda bothers me that these games come with existing configurations and high scores that aren't in the original release of the games.

For example, in Pinball Dreams II, there's a bunch of 'AAA' scores on the tables and the controls are somehow set to 'Ctrl' instead of 'Shift'... even though the in-game instructions says to use shift, and you can't configure them.

I really didn't expect this kind of thing from GoG, it feels like they just uploaded a copy that was sitting around on their hard drive or something, with their own high scores still on it!

Your point is valid. Here is the discussion:

http://www.gog.com/en/forum/pinball_gold_pack/a_rushed_release_a_little_faq