FYI, on my Steam install (Windows, latest non-beta, package version 1579321278) adding and removing games to/from existing collections (even using the new drag & drop way) is still reflected in the file just fine. Only thing that doesn't seem to be reflected for some reason is adding a game to a new collection (but creating a new collection and THEN adding a game is).
I'm not sure if the client updating the file is a left over from the old UI's code, or if this is actually intentional behaviour and the lack of a file update when adding to a new collection is a bug.
Modifying the file also does not automatically update the collections in the Steam client, though they can be manually updated to reflect the changes in the file by running "steam://resetcollections".
when I tried new UI my categories dropped to week old version while file had up-to-date categories. then once reverted back to old UI my categories are up-to-date again. new UI uses own ways and it was confirmed by steam support. I don't have a link to discussion, but user asked support how to backup his categories, support told him it is not possible with new UI because they no longer use old file and all data goes in code (they read from server, display in your library). also if you switch to offline you will miss your categories - maybe that's because offline mode can't read it from server.
maybe steam would refine offline mode someday and will add file storage back at some point. but so far this feature is broken for new UI