Fixing Boolean CLI parameters

closes #3464

- Explicitly set Boolean CLI types to true if they are presenet
- Simplify logic where these parameters are used
Wait - I just thought of something - can the default ever be `true` here?  If so - what happens?  As far as I can tell your code only sets the values to true if they are found... and doesn't set them to false if they're not found (or explicitly set to false?)