Are you talking about embedding this sort of functional noise into a line being used by ethernet? and yes most quality switches would try to clean up the noise in order to secure the data unless it just created enough of an interruption to just disrupt the connection as a whole.
RJ45 is a socket type so you can wire it to do whatever you want. you can use cat 4,5,6 cable to transport anything you want. I know multiple sites that wired ethernet cable for POTS just because it gave them the ability to do a number of things based on need.