I know it will cost you money to go do the interview, but I would say do it anyways. It will only give you more options. The worst case is they pick somebody else, but you'll still have your option to accept or decline the offer if they give it to you.
You might get a better or worse impression of the operations when you do interview, so take every opportunity to ask those questions that matter to you the most. If they are a good flight department they won't feel uncomfortable with you asking questions. They want a candidate that is a good match, just like you are seeing if their operations are a match for you. If you don't feel comfortable working for them, then just say thank you but no.
Plus it will expose you to a corporate interview since you don’t have that experience. No matter which path you take, good luck.