There are also examples of where it does, like when Dax takes command of the Defiant during the dominion war. There is a whole conversation with between O'brien and a very confused Nog about why Dax is being called Captain. Also I believe there was a couple of instances of this occurring in TOS. In the examples that you provided, Paris and Tucker should have referred to themselves as Acting-Captain, if we are to believe that Starfleet follows the traditions of modern Navies which they seem to when it suits. Trek is pretty inconsistent with how they portray starfleet at the best of times. Sometimes they follow Naval tradition and sometimes the writers ignore it for various reasons