No, I think we're using words the same way. I disagree with your statement that all or most groups "think of their own beliefs as being well thought out (i.e. rational).". They think of their beliefs of being right, but not well thought out.

"Well thought out" should mean:

1. Being arrived at through thought (science, philosophy, discovery, invention), rather than writing the bottom line first and justifying it later or not at all (revelation, mysticism, faith deliberately countering evidence, denial of the existence of objective truth).
2. Thought out to its logical consequences, without being selective about which conclusions you adopt or compartmentalizing them, making sure there are no internal contradictions, and dealing with any repugnant conclusions.