save a file to /usr using Mac's Save As dialogue
It does indeed appear to be a regular save dialog, so once you've expanded it (the down-arrow next to 'Where' so you get a mini-finder view), the key combo ⌘ Command⇧ Shift. should toggle invisibles.
(The same combo works in Finder proper, also)
In standard Open and Save dialogs (and in the Finder), you can press Command-Shift-G and then enter the unix-style path to the folder you want (e.g. "/usr/local/Cellar/apache-spark/2.3.1/conf"). Note that tab-completion works here, so you don't actually have to type everything.