If you're designing a system that will be displaying things in a monospace font, making it automatically add additional spacing may be reasonable but that is itself an application of the rule! If you're using an existing system (or, say, laying out a poster in a monospace font), then the notion that "you should ignore the rule because to do otherwise would be confusing content with presentation" is a confusion of another kind.
One place I'm a bit torn is comments in code, but I think I come down on the side that says "my editor shouldn't be trying to guess which comments are simply paragraphs of text and which may have things I'm trying to line up - monospace should work like monospace" and in this case you should be adding two spaces for clarity.