One set of pumps being on is unusual, one set being off is unusual. That's why the amber shows for prime on, and main off.
It's the unusual status that's shown in amber - some pumps are usually on, some usually off.
Even if the sense of warnings seems illogical, it can become familiar and be acted on in the correct way.
With at most 1000 feet to play with, and no power, at 100kt (50m/s), what is the maximum time to the ground? Assuming 500kW is needed to maintain level flight at that speed, that's going to come from the descent of a 2500kg aircraft at 20m/s, or from bleeding the forward speed off over 8s. It takes about 10s to cover 1000 feet at that 20m/s.
Time was not of the essence.
It's certainly possible that the prime pumps were turned on in the descent, but I suspect a landing site was the first thing on the crew's mind.