SWA will specifically want references from people who can attest to your flying abilities, but some of your references can be character references as well. I don't think it matters which one the internal rec is as long as they know you well enough to speak knowledgeably about you, your work habits, your personality, etc. If that's all you have, then go with it. It won't hurt you unless they call your reference and he denies knowing anything about you

Also, flying "with" someone means different things at different places. I might have flown once or twice in the same plane as some of my USAF friends, but I "flew with them" for years in the same squadron, seeing their results and professional attitude every single day. A guy at another airline that I went through training with, I "flew with" him for 2 months in training and never saw him again. I think the HR people know that there are going to be variances in how well a reference knows you. Remember, they're looking for more than just someone who can attest that they sat next to you in a plane and you didn't suck bad enough to crash