Your problem with a dead remote is the only one I have read about so far.
Dead or malfunctioning trains new out of the box is not uncommon. Many problems are traced to changes in manufacturing and quality control issues in the far east.

Since you bought your train set open box, the set may have been sold and returned with or because of, the dead remote.

My opinion on LionChief/LionChief Plus is that it is good for Lionel. These sets get newcomers into the field of remote control Lionel trains at an attractive price without needing to purchase additional equipment like the Legacy system needs. Since everything today is remote control, the system is attractive to young children, allowing them to be interested in and operate trains they might not otherwise be interested in.

Dealers will probably not stock any spare remotes, as there are different remotes for different locomotive types, ie. Camelback, Hudson, Pacific, Mikado, Scout, FT, GP20, NW2, RS-3. Each set or separate sale locomotive will have its' own remote, and spares will need to be ordered directly from the factory, as you have been told. I doubt you will find a remote for separate sale at a show or any dealer.

Larry