You're seeing the development process live with early access so inconsistencies happen as a result of the creative process which involves a lot of iteration. They are indeed not supposed to be treated as prisoners at that stage - though for all practical purposes they are. In subsequent updates you shouldn't find the word prisoner anymore.
As for the weapons - we are still debating that. We know it is an inconsistency but it breaks the tutorial flow if we get you to the equipment screen too fast.
