One of the possible scenarios he mentions is that if it encountered a vigorous updraft in a fledgling cell, of which there were quite a few developing at the time, then it wouldn't show on the radar, as the precip wouldn't have had time to develop yet.
As I commented earlier, these cells are not uncommon in the ITCZ in my experience. I leave it to others to discuss at length the radar theory.
If the ACARS messages were sent on HF, there is a possibility they were logged by a hobbyist. I would guess the most likely ground squitter would be Albrook. ADS-B would be out of range of ground stations at 1090 MHz but the final track may have been recorded by airborne assets, many coastal areas are patroled by AWACS type aircraft. Some areas, like the western NOPAC, have you keep your squawk after normal radar contact is lost for this reason. Or, so I've been told. With ADS-B, the aircraft sends out a unique identifier regardless of the mode 4 setting.