Here's the contents of Bay1 after my first pirate encounter: 30 t total -- 28 t of 'assorted cargo' + 1 t each of Gold (7 kg) and Platinum (11 kg). No problem there.

However, these are the reported contents of Bays 2 - 5...

As you can see, the Gold and Platinum appear in every bay. And it gets more complicated. Since Bay 1 was full, I switched to Bay 2 and carried on scooping, picking up 1 pod of Radioactives, 1 pod of Minerals and 1 pod of Gold (14 kg). Bay2 now looked like this...

5 t total -- 2 t 'assorted'; 2 t Gold (7 kg + 14 kg); 1 t Platinum (11 kg). Re-checking Bay1 shows an apparent anomaly, however...

The Gold and Platinum are still shown here (as in all the Bays) but now the amount of Gold has increased by 1 t. To 'make room for it', I seem to have lost 1 t of Alien Items.
I've repeated this test several times and it appears to function consistently in this fashion -- Gold, Platinum & Gem-Stones appear in all the bays, and scooping further 'precious' cargo displaces 'non-precious' pods from full bays.
I've searched to see if this situation is known about, but can't find anything. Apologies if it's been discussed previously.