Same here, no "pencils" at all, additionally some, but not all "description-only" items (green cubes with text, cannot be picked up) are missing. The one at the crashed transporter is placed incorrectly (to the left of the correct location), the "camp site" description on the same screen is missing, as well as the "pencil item" to the left. Other descriptions seem to be placed correctly, if they are shown at all. According to several walkthroghs, here should be gold at the beach, rhis is also not shown, as well as the wallet item at the abbey.
"-force-vulkan" gives a misleading output here:
Player data archive not found at `/usr/local/lib/games/GOG/BEAUTIFUL_DESOLATION/game/desolation_Data/data.unity3d`, using local filesystem
After that the programme ends without starting the gui.
It was visible at first, because I've managed to get code for Penrose from it.
It was probably not visible, because the Penrose code page is added automatically, not by "picking up a pencil item".