There was a small problem (which was probably related to the one mentioned by Seth above): I installed with the lite installer and left the 3d models uninstalled. The new path variables were added but the new 3d model path pointed to kicad\ folder instead of kicad\5.99. This means that if I wouldn’t have noticed it and installed the library later, KiCad 5.99 wouldn’t have found the library or would have found it in the wrong place.
Re-installing from scratch with all libraries (also deleting the old 5.99 user configuration from %appdata%\kicad\5.99) helped. I recommend that for easy transition. It takes care also of the library tables which was mentioned by chschlue above.
If you install 5.99 for the first time alongside 5.1 or start from scratch, remember to uncheck the “Import library configuration” option if you want to import 5.1 settings. Otherwise you’ll get the wrong library tables and may use 5.1 libraries with 5.99.
However, there’s still a problem with the 3D libraries: in old designs the footprints embedded into the board file refer to the old library path. You may need to add the old KISYS3DMOD variable and point it to the wanted 3D library folder. (I think this is why the original blog post announcement was taken down for a while. Let’s see what kind of instructions they’ll give us later.)