Yes. I've visited that area twice, and not seen any mid-train helpers, but rear (and sometimes front as well) manned helpers were commonplace on the heavier trains.
Anyone know if the train in question had helpers on the rear or not?
They don't ignore it - there's rules about placement of empty cars in train consists, particularly for high centre-of-gravity cars like those empty centre-beam lumber (cut timber) cars. It's certainly not a new problem e.g. decades ago Santa Fe (ATSF) spent a lot of money re-engineering the line over the summit of Cajon Pass in California, mainly because they were having too many 'stringlining' incidents around the orginal sharp curve at the summit, as trains had got heavier.
For anyone not familiar with the Horseshoe Curve area, this some of my video from nineteen years ago, taken at the same place (the viewing area) as the Virtual Railfan video - the helper locos back then were pairs of EMD SD40-2/SD40E, nowadays AFAIK pairs of big GEs.