LibreOffice typically basically has just one gtk widget per top level window and draws everything you see itself, using the gtk themeing apis to make what it draws look like they do in gtk.
But there are some truly native gtk elements. Some of them new.
Tooltips, like the above transparent example, are real gtk tooltips now. Here's what they used to look like
We recently in master began using GtkPopovers for informational messages such as the above calc formula formatting help.
As of today, context menus are native Gtk menus. This has the advantage of making managing overlarge menu scrolling all a gtk issue instead of faffing around endless in vcl to emulate what a native gtk menu would do. Flipping on/off mnemonics depending on keyboard input or whether the menu was launched by keyboard instead of mouse similarly becomes "someone elses problem". Here's the same menu launched via the menu key, automatically with mnemonics on start.
The menubar and menus launched from that menubar are currently still emulated ones, but they're the next target for nativization. We have mechanisms in place for the MacOSX and Unity menu integration that can probably be adapted and extended to support driving a native GtkMenuBar hosted in the GtkFixed-alike toplevel widget that fills each toplevel window.