For the record, my methodology here has been to create a GUI that allows for all inputs to the register_post_type() function to be passed to that function. That does not always mean I know exactly what those inputs are for, however. I just see that the register_post_type() function requires a string or a boolean etc. and I try to make my forms in the plugin pass that data as transparently as possible.
I really dislike how WP implements URLs, and I find the rewrite slug to be poorly conceived. I've had bad luck using it myself, if that's of any consolation. I'd look to the official WP docs for discussion as to what the various inputs are for. As of yet, I haven't had to create any sites that required full custom URL support, so the CCTM plugin doesn't offer much explanation on how or why you'd use some of these or even worse, it may be inadvertently sabotaging other WP functionality. If that's the case, please file a bug and I'll add a few test-cases to my unit tests.
Hope that helps illuminate the issue a bit.