The co-ordinates and depth refer to the modelled focus (or hypocentre) and the epicentre of an earthquake.
You are correct in that faults can rupture along a plane, but the location and depth information given in an earthquake report is typically based on a point source model. The focus is assumed to be where the rupture begins, with seismic waves propagating outward from there, so the arrival of these waves can be used to calculate its location. The epicentre is directly above the focus on the ground surface and the focal depth is the distance between the two.
The USGS gives some background about the information they (and equivalent agencies in other countries) provide in earthquake reports here: https://earthquake.usgs.gov/earthquakes/eventpage/terms.php
There is a diagram here, and in the link given by a previous commenter illustrating how the focus relates to the fault plane: https://en.wikipedia.org/wiki/Hypocenter.
Here is some information from the USGS about modelling a point source location: https://www.usgs.gov/faqs/how-do-seismologists-locate-earthquake?qt-news_science_products=7#qt-news_science_products