Sure, it's safe--or it can be! I believe Heather even has a Babaganush recipe/interpretation. It's so yummy pureed--really creamy. I know it would be great with pita or flatbread or baked tortilla chips. It's a divine potatoe condiment or dressing/dip for carrots!
Perhaps eggplant seeds in eggplant chips aren't as bothersome (at least to me) because they are baked. I prefer to peel the eggplant, too.
The beautiful thing about eggplant is that it compliments veggies such as mushrooms and zucchini so well, in so many ways.