master uses Gtk+ 2, gtk3 uses Gtk+ 3.
Gtk+ is the program which contains all the frames and buttons and other user interface objects which we design the user interface from.
Currently all bug fixes and new features are first made to master, and once every few days they are copied into gtk3. This “copying into” is called “merging”. In the not distant future we will abandon Gtk+ 2 and use only Gtk+ 3, so it’s better if you use and report bugs in the Gtk+ 3 version. Every time I merge, all the features and bug fixes from master are copied to gtk3, so one catches up with the other, and at those times they are essentially the same, except for the fact that gtk3 uses the more modern user interface program.
See the merges in a graph: Network Graph · Beep6581/RawTherapee · GitHub