I’m not sure if there’s a workarund in Encore.
You may want to try this in Premiere;
create a 1280×270,59.94 sequence and copy/paste the clips from the original(960×720) sequence to the new one. Add the Encore chapter markers in the new sequence and do Send to Encore.
(or)
Export Mpeg-2 DVD (widescreen) out using AME in Premiere and import the files into Encore.AME preserves the chapter markers while exporting a sequence with markers.