does the planning system have to be rational?
Pretty much. Decisions have to be in accordance with policy, and policy has to be found to be sound and in accordance with evidence.
Which is not to say that committees don't sometimes take odd decisions for political reasons, but where these are decisions to refuse they can be overturned on appeal (there's no appeal against granting permission). Or an unsound policy can be overturned by inspectors or, I imagine, at JR.